Soqotra - It is on the Yemenite tentative list. Botanically it is one of the most special sites on Earth.
I know I'm not supposed to propose sites from my own country (and there are quite a few I would) - but at least three natural ones I can't avoid (don't count my vote for these ones though :)
The Dead Sea could be proposed as a cross-boundary whs (Jordan and who knows even Palestine). It is world unique - the problems are first the political situation on its west-northern shore (Palesinian occupied territory) and the terrible industrial use Israel is making of the southern bit which has almost completely disappeared in the meanwhile.
The erosion cirques (Israel and Sinai in Egypt) are on the Israeli tentative list. They too are geologically unique. The problem is probably the military use Israel is making of large parts of the biggest ones - the Ramon Cirque.
Ayalon Cave - was discovered near Tel-Aviv a few years ago. The life inside it shows an entire eco-system existing with neither daylight nor oxygen. Similar caves had been discovered in Romania and mexico before so a cross boundary serial nomination is possible too. These sites are not even on the tentative lists of these countries.
Last of my candidates is not in an independent country so it can't be proposed. Jericho is considered the oldest still standing city in the world!

Every one sounds interesting!!

SOCOTRA
I haven't visited but do know someone who lived there doing a project for 6 months. The List undoubtedly needs a "full set" of botanical niches but the problem is how small and specialised should they be. Like the Granitic Seychelles it is, unusually for an isolated island, of Continental origin. Its flora (and some of its birds and bats) are endemic and "Endemism" is a key UNESCO natural criterion. A problem with our "50 missed list" is that we are going to be looking for "wow factor" sites and a few prickly shrubs don't exactly provide this! We need to include some of the most important "missed" natural sites however and I would support this one. It may not matter as it could be inscribed this summer anyway!

DEAD SEA
I had to do a double take on this one - first of all "surely not" then "Why not"? Well as regards endemic species it is pretty well, as its name suggests, "dead" (a few algae etc). The ecology of the desert lands around it is pretty well represented already. Geologically it is of interest and, I understand not totally explained by geologists. On the whole however I wonder whether some of the African rift lakes are not mor significant naturally?

The CIRQUES
I don't know enough to comment

AYALON CAVE
Well it is certainly going to score highly on biodiversity. I can't quite get myself to put it among the top 50 yet however!

JERICHO
I had been thinking of this one myself (I went there back in 1964 when it was "part" of Jordan). There are a few sites considered very significant in Archaeological terms from around the Neolithic period which haven't made there way onto the list. Those which have seem to be a bit peripheral - eg Chirochoitia in Cyprus and Ban Chiang in Thailand. Why isn't Çatalhöyük with its indications of the earliest agriculturalists on? And certainly Jericho too. I concede that I may be giving too much weight to achieving a full representation of the world's seminal Archaeological sites but I would support Jericho and may yet propose Çatalhöyük!!

Dead Sea - could need some expert opinion from the field of geology mainly in comparison to the African rift lakes of which I personally have no clue.

The erosion cirques of the Negev and Sinai are a geological phenomenon found exclusively in these areas (apart from a single cirque in Turkemenistan). As it's not represented yet I think it could make it to the top 50, but again a geologist review could indeed shed some light as to the site's global importance.