I think it could be worthwhile, now that we have the current top 50 missing, to go through the gaps and see whether we could come up with any interesting suggestions (and therefore I now moved this text to a new topic page).
I came up with a list in the past, but there is still a lot of work to be done, extending, modifying and specifying it. For some of the natural sites, as some members commented, there is no specific reserve mentioned. Some other gaps have been ignored (some cultural gaps for which I had no ideas). Some thematic studies (marine sites, astronomy, deserts) have also been ignored.
This summed up, I think we could try to establish a list of suggestions for filling up each of the gaps. In order to do so, I thought of compiling a list of all the gaps discussed so far:

Cultural gaps:

A:
1) pastoralist cultures
2) traditional production of crops such as wheat, barley,
maize, millet, cocoa, cotton, rubber, or fruits
3) historic and traditional irrigation systems
4) human seasonal migration (transhumance)
5) sacred and/or symbolic significance of certain natural
features such as mountains, volcanoes, forests, groves, etc
6) African, Asian and Pacific vernacular architecture
7) Non European technological properties
8) pre-industrial revolution technological properties (mining sites excluded)
9) sites representing Islam, Buddhism, Hinduism, and Judaism
10) modern heritage
11) cultural landscapes in Arab countries
12) African archaeology, rock art, cultural routes and burial sites

And now to category B:

1) Ancient Mesopotamian cultures
2) Anatolian cultures
3) Ancient Egypt
4) Seljuk and Ottoman Empires
5) Central Asia (cultural)
6) Pacific except Australia (cultural)
7) Central Africa (cultural), e.g. Bantu states
8) Post independence sites from the Americas
9) Precolumbian cultures (except Mayan)

and category C:

1) expressions of oral traditions,
music, education, philosophy, health and justice
2) rural settlements
3) modern towns (19th century onward)
4) necropolises
5) industrial landscapes
6) Zoroastrianism
7) living indigenous beliefs
8) hunting-gathering-fishing
9) places of mythical origin (whatever this should mean!)
10) cultural routes
11) migration-nomadism-slavery
12) land roads
13) aviation
14) energy conversion and utilisation (wind power,
water energy, steam, coal, electricity, thermonuclear energy,
etc.)

rock art thematic study:
http://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CCwQFjAA&url=http% 3A%2F%2Fwhc.unesco.org%2Fdocument%2F104947&ei=2jgSU_LdI-WV7AaslICgCQ&usg=AFQjCNF8KECv -6SfmtlmZuXHE2MYgdv87w&sig2=1MTLIrCJdjLOoWDl7Q8LxA&bvm=bv.62286460,d.ZGU
Pecos River

astronomy thematic study:
http://www2.astronomicalheritage.net/index.php/thematic-study-content

Caribbean cultural sites:
http://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CC8QFjAA&url=http% 3A%2F%2Fwhc.unesco.org%2Fuploads%2Fevents%2F66-report.doc&ei=5DYSU-jIA-i47AbY9oCIBA&u sg=AFQjCNEVp12hhJIXaEE2ecBawkx8ZkOKfw&sig2=zVLBRiuUeDWju0gMNFDx2g&bvm=bv.62286460,d.Z GU

Natural sites:

A
1) cold winter deserts
2) tundras
3) polar systems

B
1) Andaman
3) Benguela Current
4) Central Asian deserts
5) Fiji (marine)
6) Gulf of California
7) Karoo desert
8) Madagascar moist forests
9) Maldives-Chagos atolls
10) New Caledonia dry and moist forests
11) Palau
12) Red Sea
13) Soqotra
14) Sudd-Sahelian savanna and flooded grasslands
15) Tahiti
16) Volga and Lena river deltas
17) Western Ghats

And now to habitats (C):

1) Cape Floral
2) Okavango (and Sudd)
3) Eastern Arc Mts
4) Atlas Mts
5) Rift Valley Lakes
6) tropical mangroves of Kenya, Mozambique and Tanzania
7) Namib and Kalahari deserts
8) Somali-Maasai savannah
9) Sub-tropical forests of Cambodia
10) tropical montane forests of Sumatra, Philippines and Sulawesi
11) temprate deserts of central and eastern Asia
12) shrubland of the southern Caucasus
13) shrubland and savannahs of Southwest Australia
14) rainforests of Polynesia and Micronesia
15) mangroves of Eastern Papua and Northern Australia
16) Californian shrub
17) Central Mexico desert
18) rainforests of Southern Chile
19) Mosquito
20) temperate forests and shrubland of Central Chile
21) grasslands of Falklands and Tierra del Fuego
22) tropical Andes
23) coastal deserts of Chile and Peru
24) South Georgia
25) European saline wetlands
26) maquis
27) montado of Portugal and Spain

thematic study geology:
http://whc.unesco.org/uploads/activities/documents/activity-504-1.pdf
1) tectonic and structural features
2) stratigraphic sites
3) meteorite impact
4) deserts

thematic study deserts:
http://data.iucn.org/dbtw-wpd/edocs/2011-006.pdf
1) Lut Desert
2) Western Desert Egypt
3) The Chotts
4) Thar Desert
5) Band-e-Amir
6) Las Parinas
7) Ennedi and Tibetsi
8) Atacama
9) Gobi
10) Wadi Howar
11) Sabkha
12) Badain Jaran
13) Arches
14) Colorado Plateau
15) Death Valley
16) Lake Bonneville
17) Bodele Depression
18) Kimberley Mts
19) Hunza Valley

thematic study marine sites:
http://whc.unesco.org/en/marine-programme/
1) Scotia Sea
2) Agulhas
3) Easter Island
4) Benguela
5) Gulf of Guinea
6) Arabian Sea
7) Central Indian Ocean Islands
8) Humboldt Current
9) Northwest Atlantic

I would be happy to start with the cultural gaps in B.

1) Ancient Mesopotamian cultures:
The major Mesopotamian cultures are the Sumerian, Akkadian, Babylonian and Assyrian. These major civilizations are now only represented by a single WHS: Ashur.
Major Sumerian sites: Ur, Uruk, Eridu, Nippur, Lagash and Mari. All of these cities were later occupied by the Akkadians and the Babylonians
The location of the city of Akkad is unknown. The most significant city related to the Akkadian culture is Ebla, which is outside Mesopotamia.
Babylon was the capital city of the Babylonian Empire.
The major Assyrian cities are Ashur, Harran, Nimrud and Nineveh.
Of all these sites Nimrud, Nineveh, Harran, Babylon, Ur, Ebla and Mari are on the T lists (Mari and Ebla are in Syria, Harran in Turkey and the rest in Iraq). In order to fill up the gap Ur, Mari, Ebla, Babylon and one of the later Assyrian sites would probably have to be included.

2) Anatolian cultures:
Anatolian cultures include (chronologically unordered) the Lycians, Phrygians, Hurrians, Hittites, Assuwans, Lydians as well as neolithic sites. The most important sites are Troy (Assuwan), Ephesos (Lydian), Gordium (Phrygian), Erbil and Ahlat (Hurrians), Hattusha (Hittite), Dalyan (Lycian) and Goebeklitepe and Catalhoeyuek (Neolithic). Of these Catalhoeyuek, Troy and Hattusha are WHSs. Nonetheless, all other sites are on the Turkish T-list (except Erbil which is on the Iraqi T-list). The Turkish T-list even lists some further more minor sites belonging to these cultures. In order to fill up this gap sites representing each of these cultures would probably have to get inscribed.

3) Ancient Egypt: The most significant missing sites are on the T-list: Siwa, Fayoum, Amarna and Dahshour. Ancient Egypt currently has three WHSs. It was such an important ancient culture that it probably deserves at least several more nominations.

4) Seljuk and Ottoman Empires: Since the publication of the gap document several Ottoman sites have been nominated (Edirne, Visegrad, Butrint, Mostar). Other major Ottoman sites include Istanbul and Saftanbolu. A missing site would be Bursa which is the origin of the Ottomans.
The Seljuk Empire is currently represented only by Dvirigi. Konya is meant to fill up this gap.
Both Konya and Bursa are on the Turkish T-list and would have to be included to close this gap.

5) Central Asia (cultural) - With the expected nomination of the two silk road entries this gap is probably going to be closed. The major cultural sites from this area have now been nominated (Merv, Bukhara, Urgench, Turkestan, Khiva, Samarkand, Nisa). Other sites are the Neolithic Sarasm, the sacred Mt Soleyman-To and the rock art of Tamgaly.
The postmodern architecture of Astana could be an interesting contribution.

6) Pacific except Australia (cultural) - This gap involves several sub-categories: Pacific archaeology, living indigenous religions, colonial and modern heritage, agricultural practices and vernacular architecture. I will address each of them separately:
Archaeology - Major sites are the Lapita sites from Tonga and Samoa (T-list), Rapa Nui (inscribed), Nan Madol, Micronesia (T-list) and Raiatea, French Polynesia (T-list).
Rock art is represented in Rock Island (Palau) and Roi Mata (Vanuatu).
Living indigenous religions - Probably best represented by CLs. Represented on the list with Tongariro (NZ) and Roi Mata (Vanuatu). Manono CL (Samoa) is on the T list. Papuan religious practices are not currently represented (Trans-Fly and Sepik on the T-list could relate). The rock money of Micronesia is on the T-list of Palau and Micronesia.
Agricultural pratices - Kuk (PNG) is currently the only WHS. Houn (PNG) is on the T-list. No sites from Polynesia, which is a major shortcoming.
Modern and Colonial sites: Levuka (Fiji) and Bikini (Marshalls) are WHSs. Napier (NZ) is on the T-list.
Vernacular architecture: Most prominent examples are from Papua, e.g. the Korowai tree houses that are unique in the entire world (West Papua). No such sites are on current T-lists.
To close this gap several further nominations would be necessary. Nan Madol, Lapita sites and Rajatea are probably compulsory. Indigenous CLs, Polynesian agricultural practices and vernacular architecture have to be elaborated. Examples of postulated CLs are presented in http://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CEAQFjAC&url=http% 3A%2F%2Fwhc.unesco.org%2Fdocument%2F10061&ei=u1oSU7HWMOSK4gT2nYDwCA&usg=AFQjCNHVqgaZ3 NgqJwuqbMjD8y1hiH28fg&sig2=liphfQ_kcwROKMAFVhDQ0g&bvm=bv.62286460,d.bGE.
Only one of them (North Kohala, Hawaii) represents Polynesian agricultural practices. None include examples of vernacular architecture.

7) Central Africa (cultural), e.g. Bantu states:
Currently only Lope-Okanda (Gabon). There were three Bantu states: Kongo, Luba and Lunda. Only Kongo is on the T-list: M'Banza Kongo (Angola). The other two are not represented. The less known kingdom of Mbe is on the Rep. Congolese T-list.
Colonial sites are represented on the T-list: Albert Schweizer Hospital (Gabon), Loango (Rep. Congo) and churches (Angola). Cultural landscapes (Minkebe, Gabon) and rock art (DRCongo) are present on the T-lists.
In order to close up this gap several nominations are necessary: M'Banza Kongo and some Luba/Lunda site for the Bantu kingdoms and at least some colonial site.

8) Post independence sites from the Americas: I shall skip this category as all independent states in the Americas are relatively new and fall under the categories of modern heritage, modern town planning and non-European technological sites.

9) Precolumbian cultures (except Mayan): Major cultures are Inuit (Eskimo), Mississipi, Pueblo, Olmec, Zapotec, Aztec, Intermediate Zone, Taino, Amazonian, Chachapoyas, Wari, Inca, Moche/Chimu, Paracas/Nazca, Tiwanaku, Pachacamac, Caral, Chavin, Chinchorro, Atacama, Palaeoindian.
Some of the cultures are (well) represented: Pueblo (Chaco, Taos, Mesa Verde), Mississippi (Cahokia), Zapotec (Monte Alban, Mitla), Aztec (Mexico City, Teotihuacan), Caral, Chavin, Tiwanaku and Nazca.
Inuit is a living culture and has some T-list entries (Canada, Greenland) for CLs.
No Olmec sites have been left authentic and worthy of inscription.
The Intermediate Zone is represented by Tierradentro and Agustin (Colombia). Ciudad Perdida (Colombia) and Guyalbo (Costa Rica) are major sites that are missing. CP is on the T-list. Guyalbo was on the CR T-list and has been removed.
Taino culture is not represented and has no T-list entries. The most prominent site is Caguana (Puerto Rico).
No Amazonian sites are present. The most prominent one is Kuhikugu (Brazil), not on T-list.
Rio Abiseo has some Chachapoyas representation, but the major site of Kuelap is missing (on T-list).
Wari (Peru) is not on the T-list.
The Inca culture is heavily underrepresented, with only Machu Picchu, Cuzco and maybe Chapaq Nan next year. Some further nominations such as Ingapirca (Ecuador T-list), Titicaca (Bolivia T-list), Sacred Valley sites and Otuzco (Peru, not on T-list) are mandatory.
Chan-Chan represents the Moche-Chimu culture, but further nominations are necessary (Tucume, Huaca de la luna, Tumba de Sican - none on the T-list.
Pachacamac, Chinchorro and Atacama are all on the current T-lists (Peru, Chile, Chile).
The Palaeoindian culture is only represented in Sierro de Capivara (Brazil) and Cueva de las Manos (Argentina). The major Monte Verde is on the Chilean T-list.
In order to close up this gap multiple nominations would be necessary. Ciudad Perdida, Guyalbo, Kuhikugu, Caguana, Ingapirca, Chapaq Nan, Sacred Valley, Otuzco, Tucume, Titicaca, Huaca de la Luna, Monte Verde, San Pedro de Atacama, Kuelap and some more minor sites would be necessary.

And I proceed with natural gaps A and B.

A
1) cold winter deserts - I will now skip this gap as it is covered in the detailed desert thematic study.

2) tundras - Since the publication of the gaps Wrangel and Lena Pillars and Putorana have been inscribed (all Russia). Subantarctic tundra is also represented - Macquarie, Subantarctic Islands (Australia and NZ respectively). Northamerican tundra is represented by Waterton NP (Canada/USA). Further gaps that are particularly mentioned are South Georgia, Falklands and Svalbard. These will be discussed separately. When these are inscribed tundra will not constitute a gap any longer.

3) polar systems - Tundras have been discussed above. Non-tundra polar sites currently include Surtsey, Kluane/Glacier Bay and Ilulissat (Iceland, Canada/Alaska, Greenland). Unlike the Arctic biomes, the Antarctic ones are barely represented (only Macquarie and Subantartic Islands). South Georgia and Falkland are particularly mentioned. Further sites are on the Greenlandian and Candian T-lists. Once the suggested habitats are inscribed polar systems will not constitute a gap any longer.

B
1) Andaman - Andaman islands include two scheduled tribes: Sentinelese and Jarawa. These live in what could be defined as an anthropological reserve which has the side-effect of protecting the nature as well. Otherwise, the Andamans don't include any terrestrial reserves despite their high concentration of endemism. The marine zone is protected in the Gandhi Marine Reserve. Neither the schduled tribes nor the Gandhi Reserve are on the Indian T-list.

3) Benguela Current - Not on current T-lists. The Benguela Commission of South Africa, Nambia and Angola currently takes care of preservation.
http://www.benguelacc.org/index.php/en/large-marine-ecosystems/the-african-lmes/the-b enguela-current-lme

4) Central Asian deserts - To be discussed in the desert thematic study.

5) Fiji (marine) - Fiji currently doesn't protect its marine territory. Plans are underway for the establishment of a marine reserve.
http://wwf.panda.org/who_we_are/wwf_offices/fiji_islands/our_work/protected_areas/

7) Karoo desert - On the South-African T-list (as a mixed site).

9) Maldives-Chagos atolls - Neither are on current T-lists. Baa Atoll in the Maldives is a Unesco Biosphere Reserve. http://www.unesco.org/new/en/natural-sciences/environment/ecological-sciences/biosphe re-reserves/asia-and-the-pacific/maldives/baa-atoll/
Other atolls are well maintained, but not officially protected.
Chagos Marine Reserve protects the Chagos atolls. www.chagos-trust.org/about/chagos-marine-reserve

10) New Caledonia dry and moist forests - A major biodiversity hotspot of universal significance. Three major reserves in New Caledonia:
Grandes Fougere http://fr.wikipedia.org/wiki/Parc_des_Grandes_Foug%C3%A8res
Riviere Bleu http://fr.wikipedia.org/wiki/Parc_provincial_de_la_Rivi%C3%A8re_Bleue
Dumbea http://www.province-sud.nc/content/le-parc-provincial-de-la-dumb%C3%A9a
None of these are on the current French T-list.

12) Red Sea - The most important portion is at the Sinai peninsula is well protected in national parks. Ras Mohammad is on the Egyptian T-list. Another site further south are Suakin (Sudanese T-list). Yemen, Saudi Arabia, Djibouti and Eritrea have no sites on the T-lists.

TBC

It seems that with the upcoming inclusion of Stevns Klint, this gap according to IUCN has been fully filled.

to include Stevns Klint on the World Heritage List, this would be sufficient to recognize the K/T mass extinction and thus should not be regarded as the basis for serial extensions. IUCN thus considers it would complete an adequate representation on the World Heritage List of the phenomenon of meteorite impact.. (IUCN ev 2014)

IUCN sees the Stevns Klint as the prime spot of exposure of the Chixulub event, which can be regarded as equally iconic to the event that resulted in the Vredefort Dome.

I wonder what this will mean for the Ring of Cenotes, which are linked to the actual Chixulub crater (at the other side of the world).

And: do we know of any other meteorite impact Tentative Sites?

I have found this 2012 Danish article (In English!) which had been commissioned by the "Heritage Agency of Denmark" presumably to help them in their arguments regarding the special nature of Stevns Klint. It compares 17 sites around the World where the K/T boundary can be viewed. It also includes information about the questions IUCN would use in evaluating such a site (these were boiled down to "7 Criteria") and concluded that
a. "this report completely supports the enclosure of Stevns Klint on the Danish list of potential World Heritage Sites."
b. A suggestion that Stevns Klint should be nominated together with some other sites in Scania was unnecessary "After evaluating IUCN guidance for identifying natural heritage of potential outstanding value the K/T boundary event itself is an important time interval which stands out and can be observed at Stevns Klint without any connections with other localities."

The Cenotes in Mexico don't get a mention and only 1 site in Mexico was involved in the main comparison - appearing about half way down in the comparison list! (2 other Mexican sites are referred to in a larger list of 43 sites from which the "best 17" were selected). Interestingly the "2nd best" site based on this methodology is situated on Antarctica - and it got zero marks for "accessibility" - so it lost 4 of its 8 marks deficit c.f Stevns Klint on that 1 criterion!

http://curis.ku.dk/ws/files/44660340/Comparative_analysis_of_KT_boundary_site.pdf

It looks as if the entire nomination was put together in close collaberation with IUCN and was always going to be a "winner"!

It is also a useful document for seeing the entire spectrum of WHS related to Geological periods as of 2014 - see the table on Page 8. I haven't checked yet to see if its assignment of periods coincides with those we assigned in our own "Time Line"!!