Well, to add a bunch...
Gone:
Yapok - gone currently, but knowing DWA may appear again
Red-shanked Douc Langur
South American Sealion - from zoos anyways, there is a handful at a traveling show
Margay
Guenther's Dik-dik
Jentink's Duiker
Saiga
Coral-billed Ground Cuckoo
Jabiru
Goliath Heron
Black Heron
Guanay Cormorant
Resplendent Quetzal
Greater Yellownape
Cardinal Lory - per recent reports from SDZ, unless they're now off display
Almost gone:
Parma Wallaby - might only be one left at SDZ
Yellow-footed Rock Wallaby - LA, The Living Desert, and possibly Miami
Brown-throated Three-toed Sloth - one individual at DWA, but they might import
Black & Rufous Elephant Shrew - only a couple zoos still have them, breeding has been poor
Potto - couple zoos still have them but they're not likely to stick around
Pygmy Marmoset - not that many zoos with them now
Common Woolly Monkey - two semi-offshow at Louisville
Tree Pangolin - still at a fair handful of zoos but breeding is basically negligible
Raccoon Dog - handful at Oklahoma City
Sun Bear - pretty much all individuals left are elderly
Guadalupe Fur Seal - if SeaWorld SD still has any
Walrus - down to Seaworlds and Indianapolis
Hawaiian Monk Seal - one left at Minnesota, one in Hawaii, one at a research center in California
Aardwolf - one left at Cincinnati
Mountain Tapir - LA and Cheyenne Mountain
Barasingha - zoo population is likely doomed now
White-lipped Deer - only a few left in zoos, more privately
Musk Deer - not that many left now
Black Duiker - around a dozen left, and not breeding well
Harnessed Bushbuck - couple still at Gladys Porter
Gaur - basically reliant on Bronx for pure stock to remain in the US now
Musk Ox - down to Point Defiance in the lower 48, but there's plenty of Alaskan holders
Commerson's Dolphin - two left at Aquatica Orlando
Short-finned Pilot Whale - Seaworld SD is down to three
Tongan Scrubfowl - SDZ's lone female still lives on, but is well in her 30's
Kagu - handful of birds at three zoos, never common though
Emperor Penguin - small group left at Seaworld SD
Brolga - one or two at ICF
Shoebill - down to DWA and Tampa
Oriental White Stork - one at Louisville
Storm's Stork - down to two facilities I believe now, SDZSP and I think Bronx
Black-necked Stork - two (three?) birds left
Lesser Adjutant - Racine and Bronx, reliant on breeding
Ornate Hawk-Eagle - scattering of birds left
Gray Gull - only a few facilities left, on its way out
Parakeet Auklet - North Carolina
Crested Auklet - Aquarium of the Pacific
Yellow-casqued Hornbill - pair at Memphis
White-thighed Hornbill - one left, now in a irreputable place in FL
Purple Roller - might be gone now from SDZSP
Fire-tufted Barbet - the lone bird at SDZ I believe is the last
Plate-billed Mountain Toucan - two or three holders left
Horned Parakeet - SDZ is the only holder
Collared Lory - couple left at SDZ at most
Blue-winged Pitta - might be gone
Whale Shark - Georgia is down to either two or three now, but they were the only holder anyways
That was a pretty painful post to write... and that's not even the half of them...