1. There have been whales kept in captivity, f.e. Grey whales (JJ, anyone?) and a Mink whale in J. David Tayor also mentions narwhales in the UK in the 1960s, but i doubt that.
2.Short-beaked echidnas: Frankfurt
3. 0,0,1 Chinese Pangolin is coming to Leipzig Zoo from Taiwan; they already rebuilt the exhibit; the one in LA is dead
4. No Indris are kept in captivity at the moment
5. San Francisco now has a Sea Elephant young to foster
6. Giant armadillo has been kept at Duisburg & in Berlin, too
7. Marine iguanas have been kept at Frankfurt zoo
Animals not kept in zoos?-plenty

Just some:
-Mountain nyala (only once in the Berlin Zoo)
-Argali
-many of the duikers (Jentink, zebra...)
-Hunter's Hartebeest
-Cross River Gorilla
-Giant Forest Hog (the one in SD isn't one)
-Chiru
-many seal species, like Ladoga Seal, Hooded Seals (saw one of the last in a zoo in CDN)
-Kouprey
-Saola
-most of the cetacea
-pygmy hog
-Samoa flying fox and most other chiroptera
- Fiji Orange Dove
-Inaccessible Island Rail
-Red Colobus monkey
-Tarsiers
-quite a bunch of langurs
and many more
...