Upon request I've updated the list of WHS that have not been assigned a timeline period yet, including also the cultural WHS.

http://www.worldheritagesite.org/allnotimeline.php

If someone could solve some of the remaining issues (the ones left are quite difficult, mostly natural sites), I'd be very grateful.

P.S.: there's an update of all WHS without an official link too
http://www.worldheritagesite.org/allnolink.php

Everglades - Holocene - "Only about 5000 years ago did South Florida's climate take on its current sub-tropical and monsoonal character of dry winters followed by hot moist summers with large amounts of rain (on average 50-60 inches per year" http://www.everglades.org/early-formation/

Redwood forests - Pliocene -In its limited coastal location it "escaped" the last Ice Age. "Seqouia sempervirens had reached its northernmost limits during the Paleocene and Eocene, 65 MYA to 38 MYA. It is known to have been on the islands of Svalbard, today part of Norway and well above the Arctic Circle (Snyder 1992). During the Oligocene and Miocene, 38 MYA to 6 MYA, its range had moved south due to cooler and drier climates, and by the Pliocene it had become established in its present location" http://online.sfsu.edu/bholzman/courses/Fall99Projects/redwood.htm

Olympic - Holocene. The NP is almost entirely a "post glacial" creation " During the last Ice Age, continental glaciers surrounded the Park on all but its west side, with layers of ice up to 3,500 feet thick. This scouring by the continental glaciers created a noticeably sharp rise from sea level on the flanks of the mountains on the east and north edges of the Park. At the same time, today's river valleys were choked with floes of ice from alpine glaciers, the remnants of which dot the Park's mountains today" http://olympicnationalparkvisitor.info/mountains/glaciers/

Yosemite - Holocene - Yosemite as seen today is primarily a "post glacial" creation. "When the last glacier finally melted approximately 10,000 years ago, rock debris dammed the valley and created Lake Yosemite. Tributary creeks plummeted off sheer cliffs and gave birth to the Park's famed waterfalls. Sediment continued to fill the lake through natural processes until it eventually formed the Yosemite Valley floor." http://www.yosemitepark.com/yosemite-geology.aspx

Some cultural sites should not be too difficult to get a timeline for:

Beth Guvrin
Chauve Pont d'Arc
Erbil

Erbil - 19th C."The nominated property today consists of 19th and early 20th century mainly residential built fabric and a few public buildings, the latter largely transformed, erected on top of an unexcavated tell. The defensive wall system that would justify the appellation of citadel has been replaced by a wall of tall house façades, which happened possibly sometime between the 18th and 19th centuries. "(AB ev - remember IUCN were not very impressed with this nomination!)

Pont d'Arc - Late Pleistocene. Art going back to 35k ybp. See e.g "The only known depiction of a Late Pleistocene Ice Age leopard (Chauvet Cave) shows a coat pattern, similar to modern leopards." From wiki article on that animal

Yes - and quite a lot of them are situated in the wider "Congo Basin" area and probably have the same (or similar) "answers". So I found myself trying to establish a "time period" for this entire area!!
I ran into a few difficulties and think it is worth trying to write down a number of "principles" for asigning a time period to natural sites. I make no claims to great knowledge about geological time periods and evolution etc so would be very happy to have some input from others who are more knowledgeable in these matters than I.
a. The first principle must be that we assign WHS to the period when the attributes which were regarded as giving them OUV occurred/arose
b. However, many sites will demonstrate geological features from several/many geological periods - so we need to choose.
c. In the case of many sites what we see today is inevitably the result of quite recent geomorphological events. We need however to guard against assigning every site to "Holocene" just because they have only looked "exactly" like they do today because of events in that period. To do so would be akin to assigning every European city to "20th Century" because of its roads and street furniture!!
d. On the other hand, there are many Natural WHS whose value, whilst underpinned by rocks/strata etc set down over many geological periods, is almost entirely the result of events in the Holocene period. Such sites are particularly those "created" by the latest Ice Age and its retreat, recent sea level changes (as a result of the former), recent "dessication" and climatic changes (weather patterns) etc. An interesting aspect of assigning time periods to natural sites for me has been the realisation of just how many Natural sites have only existed a relatively "short time" having been created by Holocene events - indeed this applies to most coastal sites and those in areas which experienced the last Ice Age.
e. Some sites have been inscribed because of some particular event e.g Stevns Klint or Sardona Thrust. In such cases we should clearly choose the period when the event occurred, not the period when the evidence of that event became exposed.
f. Natural sites can be viewed as having OUV which can be categorised as "Geological" or "Biological" - Every one of course comprises a mixture of both but, whilst some possess an "equal" mixture, most will tend to lean in one or other direction. So - to take African "Wildlife Parks" (covering botanical/zoological etc values) as an example - Whilst their "wildlife" depends of course on their wider "geology" it is not for their geological value that they were inscribed. So, we need to try to pin down the period in which that "wildlife" (in the fullest "ecological" terms) became established.
g. Just as some sites are in locations which have undergone major "short term" (in Geological time!!) changes as a result of Ice Age and Sea Level change, others exist in locations which have been rather more stable across a rather longer geological period. But, the further back in time one goes, the more that some sort of geological change is likely to have occurred across that very long period. So - to take the wider "Congo Basin" sites which started this train of thought - That part of Africa has been "reasonably" stable both in terms of its geology and in terms of its wildlife genera (if not its exact "species") since the Oligocene ( 33.9 to 23 million years ago). Since then there have been periods of drier and wetter climate, there has been faulting and uplift in East Africa and there have been variuos changes in water courses as rivers became "captured" by different systems. There have been periods when the wildlife we see now has had to retreat to "refuges" followed by periods of expansion etc etc. So - how do we choose one of these periods as "representing" the WHS of this area without reverting to the "everything is "Holocene" argument??
h. For sites which are inscribed because of a single species (E.g Okapi) we should presumably try to home in on the period when that particular species evolved or (if later) moved into that area. But are e.g Virunga and Bwindi not primarily inscribed for the Mountain Gorilla even if it isn't in their name? For sites inscribed for a wider ecosystem we can use less "precise" measures (though the answer may well be the same!) trying to establish when that sort of habitat became established in that particular area (even if it has undergone shrinking/expansion etc since then)

To apply such principles to the "Congo Basin" sites. (I have tried to to cover - Garamba, Okapi, Sangha, Dja, Salonga, Bwindi and Virunga and have revisited Rwenzori)
a. " The current course of the Congo River formed 1.5-2 million years BP, during the Pleistocene" (Wiki) So "Early Pleistocene" would seem to be the "norm" for all these sites unless some "better" reason can be found on an individual site basis?
b. In the North of the Region (Garamba) - " The Northern Congolian Forest Savanna Mosaic ecoregion") - "The transition from the equatorial forest to northern latitude savannas was most probably gradual throughout the early Pleistocene" http://www.worldwildlife.org/ecoregions/at0712 )
c. But, during that period there have been plenty of changes "Central Africa has experienced repeated climatic fluctuations that have caused rain forest and savanna expansion and contraction at least since the late Pleistocene tectonics defined the Congo Basin (Faniran and Jeje 1983). It has been speculated that significant climatic shifts have occurred more than 20 times in less than 10 million years. Plants and animals adapted, migrated or became extinct with each climatic oscillation. Widespread and highly adaptable organisms that survived in islands of habitat and adapted to spatial fluidity were favored . During dry periods, savanna communities invaded far into the Congo Basin. The relatively moist riparian forests become isolated from one another and formed forest island communities in the savanna matrix . Paleobotanical evidence suggests that rain forests grew more extensively on the deeper lowland and low slope soils during wetter periods". I would propse that we ignore all these "toings and froings" and use the earliest period that the Congo sites emerged with their current ecology unless there is a good reason to do otherwise.
d. On the eastern side of the Congo the impact of the African Rift would seem to become important - e.g What gives "Virunga" particular value is its volcanism and its altitude ("Mountain Gorillas" etc) - but when exactly did that occur? See this on the Albertine Rift system - http://adsabs.harvard.edu/abs/2014EGUGA..16.5057S e.g "Late Pliocene (~ 3Ma) to Early Pleistocene (~ 2 Ma): rifting 2 - major uplift and growth of the Ruwenzori Mountains (5000 m of elevation" I see that currently we have Rwenzori assigned to "Pliocene" quoting Wiki "The mountains formed about three million years ago in the late Pliocene as a result of an uplifted block of crystalline rocks ..... pushed up by tremendous forces originating deep within the earth's crust". (Wiki). It doesn't seem unreasonable to assign Rwenzori based on its geology alone which puts it a bit earlier than the other WHS in the area?
e. But do we "assign" a time period to Virunga and Bwindi on the basis of their Volcanic/Rifting "formation" or on the basis of the evolution of the Mountain gorilla - which was much later? On this matter Wiki states "The fossil record of the area where mountain gorillas live is particularly poor and so its evolutionary history is not clear.[5] It was about 9 million years ago that the group of primates that were to evolve into gorillas split from their common ancestor with humans and chimps; this is when the genus Gorilla emerged. It is not certain what this early relative of the gorilla was, but it is traced back to the early ape Proconsul africanus. Mountain gorillas have been isolated from eastern lowland gorillas for about 400,000 years and these two taxa separated from their western counterparts approximately 2 million years ago". So do we stick with "Early Pleistocene" or move to "late Pleistocene" for the final emergence of the Eastern Mountain Gorilla? (several articles indicate that this period was the end of "Gene exchange" across the species)?
f. Regarding the Okapi reserve - wiki states "The earliest members of Giraffidae first appeared in the Early Miocene in Africa, ........ Giraffids spread into Europe and Asia by the middle Miocene in a first radiation. Another radiation began in the Pliocene but was terminated by a decline in diversity in the Pleistocene. Several important primitive giraffids existed more or less contemporaneously in the Miocene (23-10 million years ago), including Canthumeryx, Giraffokeryx, Palaeotragus and Samotherium. ..., Samotherium split into Okapia (18 million years ago) and Giraffa (12 million years ago). However, another author J. D. Skinner argued that Canthumeryx gave rise to the okapi and giraffe through the latter three genera and that the okapi is the extant form of Palaeotragus. The okapi is sometimes referred to as an example of a living fossil, as it has existed as a species over a long geological time period, and morphologically resembles more primitive forms (e.g. Samotherium". So is that Miocene, Pliocene or Pleistocene?? I am inclined to go for Pliocene based on this "The end of the Pliocene epoch (2.5-6 million years ago) saw a number of long necked giraffids evolve, but largely unsuccessfully with only 2 surving to this day" See http://www.giraffeconservation.org/giraffe_facts.php?pgid=51 (Contin

Continued from above post
g. Sanga Trinational This has been assigned to the " Northwest Congolian Lowland Forest Ecoregion " (WWF) and can be considered together with the relatively nearby "Dja Faunal Reserve". It is "special" for Bongo, Forest Elephant, W Lowland Gorilla and Chimp. As with other WHS in this region it seems to have undergone many changes across the last 2my "During the past two million years the Congo Basin Forest has frequently been reduced and fragmented in response to dry periods. Climate change in equatorial Africa is linked with changes in the upwelling of cold, deep sea water in the Gulf of Guinea. During the last ice age—some 18,000 years ago—rainfall over equatorial Africa was greatly reduced, and most of the present-day forest was actually a forest-savanna mosaic. At the time, the closed canopy forest was mostly limited to refuge areas, especially along the hills of the western coastal portions of the forest and on the far eastern mountains." ( http://carpe.umd.edu/Documents/2005/focb_aprelimassess_en.pdf ) So - we have the choice ofassigning it to Holocene to represent its "move" to its current state from its last major "dry period" during the last Ice Age OR we choose the period of its origination - Early Pleistocene.
h.Salonga. Its particular "specialism" is the Bonobo. See Wiki - "Along with the common chimpanzee, the bonobo is the closest extant relative to humans. Because the two species are not proficient swimmers, the formation of the Congo River 1.5–2 million years ago possibly led to the speciation of the bonobo. Bonobos live south of the river, and thereby were separated from the ancestors of the common chimpanzee, which live north of the river" and (also Wiki) "DNA evidence suggests the bonobo and common chimpanzee species effectively separated from each other fewer than one million years ago".This still seems to fit reasonably comfortably within the proposed "standard" period for all these Congo related forests of early Pleistocene.
i. Kahuzi Biega This park is further East "Straddling the Albertine Rift and the Congo Basin" (UNESCO) and contains 2 volcanoes so just begins to "encroach" on the Rift Valley sites of Virunga etc. Its most "famous" fauna is however still the Eastern Lowland Gorilla. Since the Mountain Gorilla evolved after this having beome separated there seems no reason to consider a speical assignment - So stick with Early Pleistocene?
j. Dja - I haven't been able to discover any reason not to assign this as per Sangha Trinational so the same issue regarding periods of dryness applies!

So a few "issues of principle" to be resolved before finally assigning all these Natural sites to a period!

I think these two (certainly Virunga) would still be WHS, even if the mountain gorilla would become extinct.
So I'd go for the formation date.

Thanks for the research, I always get a bit of a headache reading about geological processes.

Banc d'Arguin
Undoubtedly Holocene and formed first by a "marine transgresion" from sea rise following the last ice age which "invaded" the shore line and was then followed by an ongoing process of tidal and wind sand deposition. See
https://www.academia.edu/8906758/Late_Holocene_morphodynamics_in_the_littoral_zone_of _the_Iwik_Peninsula_area_Banc_dArguin_Mauritania_._J._Barusseau_R._Certain_R._Vernet_ J.F._Saliège

For Maresha / Beth Guvrin I'd go for:

"The practice of subterranean excavating as quarries and annexes for
dwellings and villages began in the 8th century BCE." (AB ev) (this is Maresha, Beth Guvrin started 2nd century BCE)

Sian kaan
"Sian Ka'an lies on a partially emerged coastal limestone plain which forms part of the extensive barrier reef system along the eastern coast of Central America. Much of the reserve lies in a zone of recent Pleistocene origin which still appears to be in a transitional stage."
And
"La Costa Maya está situada sobre un lecho calcáreo que data del Pleistoceno Tardío (hace 120,000-25,000 años)."
There has been Holocene erosion and reef formation but Late Pleistocene seems the most appropriate. The main shape of Yucatan is apparently created by earlier Cretacious limestone overlaid by later depositionsbut that doesn't seem best for this specific WHS.

Djoudj.
A wetland area of lakes, ponds and bayous situated within the Senegal River Delta, which has developed across the Holocene period following a "Marine Transgression" around 5500BP which created a large bay, subsequently filled by sediment brought down by the river. See Section 2.1 and map of changing shoreline here - https://portals.iucn.org/library/efiles/edocs/WTL-029.pdf

Lake Ichkeul
I have reached the limits of my understanding on this - but make a few notes for possible follow up (by someone else with more background knowledge??)
It appears that Lake Ichkeul and the nearby Plain of Mateur are formed by "Grabens" ( "a depressed block of land bordered by parallel faults") running SW/NE and created by the tectonic movement of Africa towards Europe.
Specifically ""Around the Jebel Ichkeul, the depression of Mateur and Ichkeul Lake are interpreted as an asymmetric graben limited to the east by the NS major fault of Messeftine"
More widely "The Tell Atlas is a major fold and thrust belt consisting of a series of nappes composed of Oligo-Miocene-aged Numidian flysch. The upper sections of the Numidian flysch were severely folded with fold axes basically trending northeast (Rouvier 1977; Cohen et al. 1980; Ben Ferjani et al. 1990). The Tell Atlas was formed during the collision of Tunisia with a continental plate to the north (e.g. the Corsica–Sardinia–Petite Kabylie continental plate)". See far more in http://gji.oxfordjournals.org/content/151/1/117.full
I have (so far) been unable to place the creation of this depression in a Geological period we are using.
That (and other) depressions became Lakes which gradually filled with sediment across the Pleistiocene (Ichkeul alone survives). A reasonably stable system then developed in which the lake became brackish/saline (though the extent of this changed many times depending on climate/rainfall) exchanging water at different times of year with the Mediterranean through the Gulf of Bizerta.
Which of all these "periods" would be appropriate is another matter - the one which created the depression into which the lake developed or a later one creating the "balanced system" (though that is now in "imbalance" because of human activity)??

3 of the African Parks remaining to be assigned to a Time Period (Comoe, Niokolo-Koba and "W" Niger) belong to the same "Ecozone" - The "West Sudanian Savanna". See - http://www.worldwildlife.org/ecoregions/at0722

A further site - that of Manovo-Gounda - in CAR belongs to the "East Sudanian Savanna" . See - http://www.worldwildlife.org/ecoregions/at0705

The above links highlight the similarity of the 2 regions
a. In their geology. Both the East and West are said to "overly a mixture of Precambrian basement rocks, and a number of post-Jurassic sedimentary basins"
b. In their "habitat structure and species composition"

I have therefore looked at them all together.
The basic geology of the area appears to have been settled very early without subsequent significant tectonic events to change it. The current ecology of the entire area is very much a result of its "climate" with limited seasonal rains. But when did that "ecology" first emerge in the area and has it remained "constant"? In fact, a problem with assigning a "time period" to all the Savanna, Sahelian and even Saharan sites, which we haven't really discussed until now, is the great variation in "wetness"/"dryness" which has occurred across the areas in certainly the Holocene period and apparently even going back (at least??) into the Pleistocene ("the climate of the Sahara, which has undergone enormous variations between wet and dry over the last few hundred thousand years" Wiki) . The current ecology of all these sites is thus only a "snapshot" - earlier rainfall patterns would have created very different landscapes and hence flora/fauna. The 2 ecoregions have low levels of faunal, but somewhat higher levels of floral, endemism - which seems to show a long period of flux during which "mobile" creatures could move in and out but which some less "mobile" flora evolved to cope with.

I have looked, so far, fairly unsuccessfully for articles/papers which discuss the climate and ecology of the region over a geological time scale. There are interesting articles on the "Neolithic Subpluvial" relating to the "Green Sahara" - e.g "During periods of a wet or "Green Sahara", the Sahara becomes a savanna grassland and various flora and fauna become more common. Following inter-pluvial arid periods, the Sahara area then reverts to desert conditions and the flora and fauna are forced to retreat northwards to the Atlas Mountains, southwards into West Africa, or eastwards into the Nile Valley. This separates populations of some of the species in areas with different climates, forcing them to adapt, possibly giving rise to allopatric speciation." Presumably when the Sahara is "green" then the area to its south is not as dry as it is when the Sahara is "desert" and would have a different ecology?

Another possible indicator of the extent to which the area must have changed in climate and ecology across the millenia is that the West Sudanian Savanna includes the area of the former "Mega Chad" lake. Wiki says of this - "For most of the Quaternary, from 2.6 million years ago to the present, the basin seems to have been a huge, well-watered plain, with many rivers and waterbodies, probably rich in plant and animal life. Towards the end of this period the climate became drier. Around 20,000-40,000 years ago eolianite sand dunes began to form in the north of the basin.[3] During the Holocene, from 11,000 years ago until recently, a giant "Lake Mega-Chad" covered an area of more than 350,000 square kilometres (140,000 sq mi) in the basin. It would have drained to the Atlantic Ocean via the Benue River. Stratigraphic records show that "Mega-Chad" varied in size as the climate changed, with a peak about 2,300 years ago. The remains of fish and molluscs from this period are found in what are now desert regions" See - https://en.wikipedia.org/wiki/Chad_Basin#Climate_and_ecology

None of the 4 sites is immediately adjacent to this former lake but a body of its size must have required levels of rain which must have impacted neighbouring areas. And the Wiki article indicates that this was the situation for most of the Pleistocene.

But that doesn't provide a definite steer as to when we regard the current ecology of the Savanna area as having been formed!! Holocene, Pleistocene ... or earlier?? So - again I come to no great conclusion on the assignment of a "Time period" to these 4 savanna//subsahelian sites. Any ideas or additional knowledge?

Serengeti
This WHS is "East African Savanna" par exellence - but when did that ecosystem develop?

It appears that rifting and lifting of the E African Plateau together, possibly, with climate change either related to it or independent of and much wider than it, are the main causes. The subject is apparently "controversial" in relevant academic circles and closely linked to theories about human evolution in the area. (Gradualism v Punctuated change).

For the "simple" standard theory see "The human lineage originated about 2.5 million years ago, coinciding with the expansion of savannas — grasslands mixed with trees — across East Africa. As such, researchers have long speculated that savannas were key to our evolution. For instance, the replacement of woodlands with savannas may have prompted the ancestors of humans to stray from trees and begin walking upright across the grass, which in turn would have freed up their hands for tool use. " http://www.livescience.com/15377-savannas-human-ancestors-evolution.html

The next reference is rather more detailed but, whilst it considers alternative aspects of the causes of evolution (covering humanoids but also many other fauna and flora) it also seems to suggest major changes in the ecology of the area particularly across a much longer period than 2.5mybp. These were associated with rifting, but also other "World wide" trends - "During the period of early human evolution in Africa there are five major transitions or climate events that would have influenced African climate: 1) the emergence and expansion of C4 dominated biomes (∼8 Ma onwards), 2) the Messinian Salinity Crisis (6–5.3 Ma), 3) the intensification of Northern Hemisphere Glaciation (iNHG, 3.2–2.5 Ma), 4) the development of the Walker Circulation (DWC, 2.0–1.7 Ma), and 5) the Early–Middle Pleistocene Transition (EMPT, 1.2–0.8 Ma).". All very complicated and "uncertain"!! (But the article may also have relevance to othe African WHS as per the above West African ones) See
http://www.sciencedirect.com/science/article/pii/S0277379114002418

Then I came cross the "2.5 million Year event"!!
See - "A well-known example is the 2.5 million year event, in which a mass fluctuation of temperature occurred 2.5 million years BP, causing a rapid burst of speciation. It was during this event, so the hypothesis states, that many species attempted to move from their now uninhabitable habitats and later developed different adaptations in their new environments, evolving into different species. An example of this is seen in antelopes after these temperature fluctuations occurred. Formerly known only to feed as woodland browsers, the antelopes were able to make a change in eating habits, eventually becoming grassland grazers. These findings further indicate rapid adaptations made by species during this event." - https://en.wikipedia.org/wiki/Turnover-pulse_hypothesis#The_2.5_Million_Year_Event

The choice would seem to be between Early Pleistocene (2.58- 1.80mybp) or Pliocene (5.33 -2.58 mybp). from the above articles etc (but without claiming fully to understand them!!) I am inclined to go for the former !!

Cape Floral Region
Pliocene (on the basis of unchanged landform since then, period of most speciation and establishment of general climate patterns as of today despite subsequent ups/downs)-
Excellent geological time line for the Cape area in this article
http://bluehillescape.blogspot.co.uk/2014/01/cape-fynbos-overview-from-paleo-history. html
with this conclusion "While the radiation of Cape clades occurred throughout the late Cenozoic, speciation was most prolific during the Pliocene. By the end of the Pliocene, contemporary Cape climates, with their steep moisture and thermal gradients, had become established. It was during Pliocene times that climatic and edaphic conditions enabled the zonal development of now widespread Cape vegetation types such as renosterveld, succulent karoo, limestone fynbos, dune fynbos and grassy fynbos"
See also
"ca. 15% of the modern species evolved during the Pleistocene, and almost 40% since the beginning of the Pliocene. We suggest that these clades might have radiated in response to the fynbos vegetation increasing its extent in the Cape as a result of climatic change." in
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693430/