There are SO many that I haven't included into my zoos yet. My main zoo has a slowly growing variety that is often added to by the community challenge, or the rewards from doing them. In fact, last night I added the Chinese Pangolin since I finally figured out how to make the burrow I wanted for them. So I think I have included maybe 20 habitat animals, and 2 exhibit.
The ones (habitat) that I know I haven't included in my zoos yet are the African Elephant, either of the crocodiles(?), Timber wolves, Bonobo, Aardvark, Tapir, Orangutan, Warthog, Panda, Himalayan Brown Bear, Hippo (either), Nyala, Siberian Tiger, Snow Leopard, Hyena, Springbok, Lion, Chimpanzee, and those from the Arctic DLC.
One day, I do plan to have all of these in my main zoo, but I sometimes find it hard to add another animal because my system decides to go alert crazy. And idiot that I am, I often leave the zoo running while I deal with the issues, so more issues pop up. Or I get too busy trying to figure out why whoever is not breeding and try to resolve that issue.