Regarding the Great Apes:

- Mountain Gorilla: found in both Bwindi and Virunga. Their numbers are similar: 340 versus 480 (source: wiki). I wouldn't want to choose one above the other on this species.
- Eastern Lowland Gorilla: only in Kahuzi-Biega
- Western Lowland Gorilla: Lopé-Okanda, Sangha Trinational
- Chimpanzee: Bwindi Impenetrable National Park, Dja Faunal Reserve, Garamba National Park, Kahuzi-Biega National Park, Niokolo-Koba National Park, Salonga National Park, Sangha Trinational, Virunga National Park
- Orangutan: Tropical Rainforest Sumatra

My conclusion of this little analysis would be:
- Bwindi: both a significant number of rare Mountain Gorrilas plus chimpanzees
- Virunga: both a significant number of rare Mountain Gorrilas plus chimpanzees
- Kahuzi-Biega: only habitat for the Eastern Lowland Gorilla, plus chimpanzees
- Sangha Trinational (bring it over from diff category): Western Lowland Gorilla, plus chimpanzees
- Tropical Rainforest Sumatra (bring it over from diff category): only Orangutan habitat on List

I think we can explain to the little green man that we are especially intrigued by looking at fauna species that are most closely related to us.

P.S.: forgot Salonga NP (bring it over from diff category) for the Bonobo (only NP where they are found)!

Just "taking stock". There were originally 33 sites in this category (ignoring any transfers which might be done) - the heading post says 34 but I can't add it up to that!!
Your last full post had 12 Y plus 6 maybes.
On average we are looking for a reduction to 40% but of course this may well not be evenly spread across all Categories (Indeed I wouldn't expect it to be). So plus/minus we are in the right ball park?
I am not saying that we should shoehorn unnecessarily to achieve 40% but it is worth just keeping an eye on what we are achieving!

Yes. But to me it seems we have just been narrowing it down without much reasoning, and choosing the better known places.
Why choose Virunga above Bwindi for example?

Reasonable question but difficulty in choosing between them shouldn't mean choosing both should it.?
What other factors could be considered?
Size?
Condition?
Number of OUV criteria? Virunga also has viii because presumably of volcanism

Virunga is said to be "... known for its exceptional (bio)diversity, containing more bird, mammal and reptile species than any protected area on the African continent" (wiki). The park was created in 1925 by King Albert I of Belgium as the first national park on the continent of Africa. It was also a very early WHS (1979), often a good sign.

So I could live with choosing Virunga over Bwindi, but I'd want to upgrade Bwindi to a 'Maybe'.

We could of course take the view that any site "In Danger" can't be one of the best 400?

No, that would be sad. We should show the positives and negatives (just as with slave trade etc)

Rainforests of the Atsinanana seems to get no support. It is a site rich in endemism. Well known for its strepsirrhini (e.g. lemurs).

This list has taken me a long time to go through. I realize that when we are setting a limit like Top 200 that we can only provide the highlights of the world's fauna, but even still I found it hard to winnow down sites. In some cases, I opted to choose sites that were on other lists because they have already gotten support for other components. In other cases, I chose sites from other categories to represent specific regions that weren't covered on this list (and I'll probably be recommending them when those categories come up for discussion). Here's the list I've come up with (sorry it ended up so long):

Africa
1. Serengeti -- savannah in eastern Africa that hosts the world's largest annual overland migration of animals, as wildebeest, zebra, and gazelles (followed by their predators) relocate in search of new watering holes and grazing areas
2. Ngorogoro -- actually covers much of the same wildlife as the nearby Serengeti, but located in a volcanic crater
3. Okavango Delta (Natural Landscape, River/Lake category) -- wetland in southern Africa that is home to a variety of birds, as well as white and black rhinoceros, elephant, lions, and leopards
4. Bwindi Impenetrable National Park -- montane forest in central Africa that is home to half the world's population of mountain gorillas
5. Dja Faunal Reserve -- rainforest in west-central Africa which includes wildlife like the western lowland gorilla and the forest elephant
6. Rainforests of the Atsinanana -- highlights wildlife endemic to Madagascar, including lemurs
7. iSimangaliso Wetland Park (Natural Landscape, River/Lake category) -- highlights marine life (including whales and whale sharks) off the southeastern coast of Africa
8. Banc d'Arguin -- nesting ground off the west coast of Africa for a diverse range of migrating birds
9. Air and Ténéré (Natural Landscape, Desert category) -- covers wildlife unique to the Sahara desert, including endangered antelope
10. Aldabra Atoll -- Indian ocean island with giant tortoises and a variety of birds

Asia
1. Socotra Archipelago (Natural Landscape, Marine/Coastal category) -- this is the closest area to represent the Arabian Peninsula (thanks to Oman), and it represents reptiles endemic to the Socotra islands, as well as migratory sea birds and marine life; the flora is more distinctive here
2. Keoladeo National Park -- important nesting area in South Asia for migratory birds from Siberia and China, including the rare Siberian crane
3. Manas Wildlife Sanctuary -- highlights wildlife found in the Himalayan foothills, including Asian elephants, Bengal tigers, water buffalo, the Indian rhinoceros, and pygmy hogs
4. Dong Phayayen -- Southeast Asian forest home to elephants, tigers, leopard cats, and the Siamese crocodile
5. Tropical Rainforest Sumatra (Natural Landscape, Forest category) -- Indonesian rainforest which is home to the Sumatran orang-utan, rhinoceros, elephants, tigers, and Malayan sun-bears
6. Golden Mountains of Altai (Natural Landscape, Mountain category) -- includes animals found on the steppes and mountains of central Asia, including the endangered snow leopard
7. Sichuan Giant Panda Sanctuaries -- highlights the most well-known of China's fauna, but also includes red pandas and endangered leopards
8. Central Sikhote Alin (Natural Landscape, Forest category) -- covers a temperate zone from taiga to subtropics in eastern Asia, and is home to the Siberian tiger and Himalayan bear
9. Wrangel Island -- Arctic islands home to polar bears, walrus, grey whales, and migratory birds

Australia and Oceania
1. Gondwana Rainforests (Natural Landscape, Forest category) -- rainforests in eastern Australia which are home to a variety of marsupials, including kangaroos, koala, and platypus
2. Great Barrier Reef (Natural Landscape, Marine/Coastal category) -- coral reefs off northeastern Australia which are home to a variety of marine life
3. Sub-Antarctic Islands (Natural Landscape, Insular category) -- highlights penguins, sea birds, and marine life found in the Southern Ocean
4. Hawaii Volcanoes National Park (Geological Formation, Volcanic/Thermal category) -- home to bird life endemic to the Hawaiian Islands, including Hawaiian songbirds and the nēnē (Hawaiian goose), as well as sea turtles

North America
1. Everglades (Natural Landscape, River/Lake category) -- located in the southeastern corner of the US, this is North America's most significant breeding ground for wading birds, and is also home to panthers, alligators, crocodiles, and manatees
2. Rio Platano Biosphere Reserve (Natural Landscape, River/Lake category) -- Central American rainforest home to giant anteaters, ocelots, jaguars, and monkeys
3. Alejandro de Humboldt National Park (Wildlife Habitat, Flora category) -- home to parrots, hummingbirds, lizards, and small mammals found on Caribbean islands
4. El Pinacate -- (Natural Landscape, Desert category) desert region in southwestern North America, home to pronghorn, bighorn sheep, and desert tortoises
5. Gulf of California -- located in southwestern North America, this marine environment contains almost 40% of the world's total number of marine mammal's species
6. Great Smoky Mountains National Park (Natural Landscape, Forest category) -- highlights wildlife from the Appalachian Mountains of eastern North America, including black bears, red foxes, white-tailed deer, raccoons, and a variety of salamanders
7. Yellowstone -- Rocky Mountain park home to bison, wolves, and grizzly bears
8. Olympic National Park (Natural Landscape, Diverse Ecosystems category) -- located in the northwest of the United States, this park is home to wildlife typical of the Pacific Northwest, including elk, bear, cougars, and beavers
9. Wood Buffalo National Park -- represents the boreal forests of northern North America, and is home to the world's largest herd of free-roaming wood bison, as well as the only known breeding habitat of the whooping crane

South America
1. Galapagos Islands -- located off the west coast of South America, these islands are world-renowned and home to giant tortoises, flightless comorants, and finches
2. Noel Kempff Mercado National Park (Natural Landscape, Diverse Ecosystems category) -- Amazonian rainforest home to jaguars, giant anteaters, giant armadillos, and river dolphins
3. Pantanal (Natural Landscape, River/Lake category) -- wetlands in southwestern Brazil home to jaguars, alligators, giant anteaters, capybaras, and a variety of birds
4. Huascarán National Park (Natural Landscape, Mountain category) -- represents Andean wildlife, including condors, vicuña, and the spectacled bear
5. Brazilian Atlantic Islands (Natural Landscape, Marine/Coastal category) -- highlights marine life such as sharks and dolphins, as well as turtle and sea birds found off the Atlantic coast of northeastern South America
6. Peninsula Valdés (Natural Landscape, Marine/Coastal category) -- Patagonian peninsula and waters on the southeastern coast of South America, which is home to right whales, sea lions, and elephant seals

Europe
1. Belovezhskaya Pushcha / Bialowieza Forest -- woodland in north-central Europe, home to wolves, European bison, lynx, and otters
2. Plitvice Lakes (Natural Landscape, River/Lake category) -- forested area in southeastern Europe which is home to brown bears, owls, and wolves
3. Gulf of Porto (Natural Landscape, River/Lake category) -- represents Mediterranean bird and marine life
4. Laponian Area (Geological Formation, Glaciation category) -- subarctic region in Scandinavia, which is home to reindeer and migrating birds

Impressive, Colvin!

I like that you made a difference among the continents, as the fauna on each will be mostly different.
There are a few disputes with the previous commentors:
- Bwindi over Virunga. They are very much alike, Virunga might just have an edge above it for me because of its long conservation history with its ups and downs
- Manas over Kaziranga. This also seems a choice between two similar sites. Most chose Kaziranga, why did you go for Manas instead?
- NZ Subantarctic islands: all 3 subantarctic sites seem to have similar fauna, though I would support picking NZ Subantarctic in the Fauna Category and Heard&McDonald for the volcanic one.

Personally I would not choose the Laponian area for fauna (reindeer here are domesticated), it's more of a cultural landscape.

Manas and Kaziranga are located in same region. Both have high bio-diversity.Indian one horned Rhino became identity of Kaziranga (though one can find them in Manas but in less no.) where as pygmy hog(their only habitat, critically endangered) became identity of Manas. It is more like choosing one animal over another.

I always support that one species should not be compared with another. There are some national parks which at least don't deserve to be out at first sight.

Bwindi- Mountain Gorilla (everyone gave second thought to choose between Bwindi and Virunga ). Both became identity for Gorilla.
Garamba National Park- Northern White Rinoceros (Only habitat)
Lopé-Okanda- Western Gorilla
Manovo-Gounda St. Floris- Black Rhinoceros
Ujung Kulon National Par- Javan Rhinoceros
Tropical Rainforest Sumatra- Sumatran orangutan

My selections:

Galapagos Islands
Komodo National Park
Sichuan Giant Panda Sanctuaries
Yellowstone

New summary. Are we there yet?

Aldabra Atoll - Example of Atoll creation plus notable bird and tortoise species
Banc d'Arguin - Representing the Eastern Atlantic Migratory (Birds) Flyway
Belovezhskaya Pushcha / Bialowieza Forest
Bwindi Impenetrable National Park - For its mountain gorillas
Chitwan National Park
Dja Faunal Reserve - rainforest in west-central Africa which includes wildlife like the western lowland gorilla and the forest elephant
Donana National Park
Dong Phayayen - Southeast Asian forest home to elephants, tigers, leopard cats, and the Siamese crocodile
Galapagos Islands - famed for their vast number of endemic species and were studied by Charles Darwin
Garamba National Park
Gulf of California
Kahuzi-Biega National Park
Kaziranga National Park - high bio-diversity.Indian one horned Rhino became
Keoladeo National Park
Komodo National Park - for the iconic Komodo dragon
Lopé-Okanda
Los Katios National Park
Mana Pools
Manas Wildlife Sanctuary
Manovo-Gounda St. Floris
Monarch Butterfly Biosphere Reserve - Spectacular butterfly migration
Ngorongoro - savannah wildlife in a volcanic crater
Niokolo-Koba National Park
Okapi Wildlife Reserve
Rainforests of the Atsinanana - highlights wildlife endemic to Madagascar, including lemurs
Selous Game Reserve
Serengeti - savannah in eastern Africa that hosts the world's largest annual overland migration of animals
Sichuan Giant Panda Sanctuaries - Giant Panda
Virunga National Park - exceptional (bio)diversity, first national park on the continent of Africa, significant number of rare Mountain Gorrilas plus chimpanzees
W National Park of Niger
Wood Buffalo National Park
Wrangel Island - Arctic + Polar Bears
Yellowstone - (already in for geothermal), add: Rocky Mountain park home to bison, wolves, and grizzly bears

Brought over from different categories:
Ujung Kulon - Javan Rhinoceros
Tropical Rainforest Sumatra - Sumatran orangutan

I just realized I'd forgotten to answer your question. I chose Manas because it was closer to the Himalayas, providing a more varied landscape, and also had a wide variety of wildlife, including pygmy hogs and a few one-horned rhinos. I haven't been to India, though, so I suppose those who have been to both parks would have a better idea as to which site is preferable.