I would like to refer to the list of filling up the gaps and recommend some sites that could address these gaps. Additionally, I shall refer to the list of missing countries and territories. I haven't got ideas for all of them so feel free to add your own.
1) pastoralist cultures - sites from Central Asia?
2) traditional production of crops such as wheat, barley,
maize, millet, cocoa, cotton, rubber or fruits - African and North American sites?
3) historic and traditional irrigation systems - Nan Madol (Micronesia), Knossos (Greece), ?
4) human seasonal migration (transhumance) - ?
5) sacred and/or symbolic significance of certain natural
features such as mountains, volcanoes, forests, groves, etc - represented in Africa and Asia. More needed from the Pacific, Australia and the Americas.
6) African, Asian and Pacific vernacular architecture - Asian and African are represented. Pacific completely missing - Papua!
7) Non European technological properties - as mentioned, Suez and Panama canals. I would add NASA and some Soviet sites. Trans-Siberian railway.
8) pre-industrial revolution technological properties (mining sites excluded) - ?
9) sites representing Islam, Buddhism, Hinduism, and Judaism - Judaism the most underrepresented. Schum nomination in Germany. Further ideas?
10) modern heritage - highly underrepresented. NASA, Chicago school, Miami art deco, Watts Tower, Munich Olympic Stadium. I further embrace hubert's suggestions for contemporary architecture. Ford, Hollywood, NASA, Moscow underground.
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 - Babylon, Ur, Nemrud (all Iraq)
2) Anatolian cultures - Mitani, Lycians, Göbekli Tepe (all Turkey)
3) Ancient Egypt - sites on Egypt's T list
4) Seljuk and Ottoman Empires - Bursa, Konya (both Turkey)
5) Central Asia (cultural) - Silk Road
6) Pacific except Australia (cultural) - Nan Madol (Micronesia), some Polynesian sites (Lapita in Samoa, Marae in French Polynesia, Tonga)
7) Central Africa (cultural), e.g. Bantu states - ?
8) Post independence sites from the Americas - Rogelio Salmona in Colombia, Eladio Dieste in Uruguay, Ford, Hollywood
9) Precolumbian cultures (except Mayan) - Huaca del sol (Moche) - Peru, Huari - Peru, Ciudad Perdida - Colombia, Guyalbo - Costa Rica, Chinchorro - Chile, Kuhikugu - Brazil, Monte Verde - Chile, Ometepe - Nicaragua, Caguana - Puerto Rico, Tenochtitlan (Olmec) - Mexico
and category C:
1) expressions of oral traditions,
music, education, philosophy, health and justice - For education Oxford and Cambridge. For justice the Nuremberg trials site. For philosophy the Kibbutz, Civil Rights Movement.
2) rural settlements - well represented?
3) modern towns (19th century onward) - ?
4) necropolises - well represented?
5) industrial landscapes - Ford, Hollywood
6) Zoroastrianism - ?
7) living indigenous beliefs - ?
8) hunting-gathering-fishing - Göbekli Tepe (Turkey) for gathering
9) places of mythical origin (whatever this should mean!) - ?
10) cultural routes - Silk Route
11) migration-nomadism-slavery - Ellis Island for migration, ?
12) land roads - the Trans-Siberian, Qapaq Nan
13) aviation - Hangar Y, Tempelhof
14) energy conversion and utilisation (wind power,
water energy, steam, coal, electricity, thermonuclear energy,
etc.) - ?
1) cold winter deserts - Gobi, Colorado
2) tundras - well represented
3) polar systems - Antarctica!
3) Benguela Current
4) Central Asian deserts - Gobi
5) Fiji (marine)
7) Karoo desert
9) Maldives-Chagos atolls
10) New Caledonia dry and moist forests
12) Red Sea
14) Sudd-Sahelian savanna and flooded grasslands
16) Volga and Lena river deltas
And now to habitats (C):
2) Okavango (and Sudd)
3) Eastern Arc Mts
4) Atlas Mts
6) tropical mangroves of Kenya, Mozambique and Tanzania
8) Somali-Maasai savannah
9) Sub-tropical forests of Cambodia
10) tropical montane forests of 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
18) rainforests of Southern Chile
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
27) montado of Portugal and Spain
1) tectonic and structural features
2) stratigraphic sites
3) meteorite impact - Chicxulub (Mexico)
Missing countries and territories:
Famagusta (Northern Cyprus)
South Sudan ?
Mariana Trench (Marianas and Guam)
Grasslands of Falklands
South Georgia (natural)
Maldive and Chagos atolls
Tonga and Samoa (Lapita sites)
Rwanda - memorial sites
Marae and Tahiti natural (French Polynesia)
Nan Madol (Micronesia)