For what it's worth, I think this might be something that European zoos tend to do better than American zoos - at least in terms of variety. Most European zoos with an African area will have some sort of smaller mammal exhibit and often tortoises or other herps alongside. Typically these species will tend to be along the lines of a non-meerkat mongoose species, Bat-eared or Fennec foxes, Naked mole-rats, any of the African spiny rat species, as well as Leopard/Spider/Sulcata tortoises. It really doesn't take much space and I find that while there are perhaps fewer crowds around these types of smaller exhibits, the people watching tend to stay longer as the species feel perhaps more tangible than a giraffe, elephant or lion. A lot of these species are quite active as well, which does make them a good choice for such exhibits.
As for pure variety, I'm afraid the best example is again going to be Plzen, at least of those I've come across. Plzen has two large houses entirely dedicated to small African fauna - the Madagascar House and the African Night House. The species lists are something along the lines of this, although this might be a bit outdated:
African Night House: Slender mongoose, Bat-eared fox, Dwarf mongoose, Banded mongoose, Common cusimanse, Gambian epauletted bat, Shaw's jird, Gaboon viper, Nile rat, Typical striped grass mouse, Four-toed jerboa, Tibesti spiny mouse, Xeric striped grass mouse, Mesic striped grass mouse, Greater Egyptian jerboa, Lesser Egyptian jerboa, Emin's giant pouched rat, Springhare, Garnett's bushbaby, Four-toed hedgehog, Cape fox, Straw-colored fruit bat, Northern lesser bushbaby, African brush tailed porcupine, Tristram's jird, Acacia rat, Matthey's mouse, Black-backed jackal, Yellow mongoose, Hausa genet.
Madagascar House: Grey mouse lemur, Malagasy jumping rat, Ring-tailed lemur, Madagascar tree boa, Hissing cockroach, Red ruffed lemur, Collared lemur, Dumeril's tree boa, Rodriguez flying fox, Red bellied lemur, Black lemur, Tailless tenrec, BAW ruffed lemur, Western fat-tailed lemur, Red tailed silverside, Kotsovato, Black diamond cichlid, Pachypanchax sakaramyi, Lac Aloatra bamboo lemur, White-headed lemur, Narrow-striped mongoose, Ring tailed mongoose, Red fronted lemur, Radiated tortoise, Common brown lemur, Oustalet's chameleon, Karsten's zonosaur, Cuvier's swift, Spider tortoise, Grandidier's swift, Broad-tailed girdled lizard, Greater day gecko, Madagascar velvet gecko.
So yeah, in terms of species variety and volume, Plzen has a brilliant series of African buildings. Prague also has a lovely African building if I remember correctly, as do Basel and Nurnberg.