Three zoos outside home range:
Capuchinbird (Cincinnati and San Diego Zoos, Dallas World Aquarium)
Nope! Also Bronx and I believe Walsrode. Edit: I see TLD posted more for Europe.
Overall:
One collection:
Black and white hawk eagle (DWA)
Versicolored barbet (DWA)
Serengeti topi (behind the scenes at San Antonio- hopefully changing soon!)
Spectral tarsier (Ueno Zoo)
Royal antelope? (SDZ)
Capuchin babbler (SDZ)
Guatemalan mantled howler monkey (Gladys Porter Zoo)
Two collections:
Southern steenbok (San Diego Zoo Safari Park, Disney's Animal Kingdom)
Papuan mountain pigeon (SDZ, Louisville Zoo)
Puna flamingo (Slimbridge WWT, Berlin Zoo?)
Andean flamingo (Slimbridge, Berlin)
Red uakari (Los Angeles Zoo, one in South America)
Three collections:
Squatter pigeon (Currumbin Wildlife Sanctuary, Melbourne Zoo, San Diego Zoo)
Eastern lesser grey bamboo lemur (Duke Lemur Center, Cincinatti Zoo, Ueno Zoo)
Emperor penguin (SeaWorld San Diego, two aquariums in Japan?)
Mountain tapir (Cali Zoo, Los Angeles Zoo, Cheyenne Mountain Zoo?)
Outside of home range:
One collection:
Jabiru (Dallas World Aquarium)
Guianan crested eagle (DWA)
Black hawk eagle (DWA)
Squatter pigeon (SDZ)
Saffron toucanet (DWA)
Resplendent quetzal (DWA)
Crested quetzal (DWA)
Curl-crested jay (DWA)
Many-banded aracari (DWA)
Brown-throated three toed sloth (DWA)
Hosmer's skink? (Philadelphia)
West African bushbuck (Gladys Porter Zoo)
Spectacled flying fox (Lubee Bat Conservancy)
Calamian hog deer (any in Europe? LA Zoo)
Two collections:
Ivory billed aracari (DWA, Philadelphia)
Black-necked stork (San Antonio, Miami- unless some I don't know about are in Europe)
Florida manatee (Cincinatti, Columbus)
Red-backed bearded saki monkey (Omaha, DWA)
Three collections:
Maguari stork? I don't know if any are in Europe (San Antonio Zoo, Audubon, behind the scenes at another)
Ornate hawk-eagle (SDZ, DWA, behind the scenes at another)
Brolga (International Crane Foundation, Whipsnade, Olmense)
Collared lory (SDZ, Zoo Parc de Beauval, The Tisch Family Zoo)
Maleo (SDZ, Bronx, Tulsa)
Extinct in the Wild:
Kihansi spray toad (Bronx, Toledo, Omaha, Chattanooga, Detroit)
That's all I can think of off the top of my head. Any corrections or reaffirmations (especially where I put question marks) are welcome!