I know this an old thread, but I do have a bit to add.
I personally think that some of the best zoo gift shops are the ones that have part of the zoo's collection inside them. For example, the gift shop at Racine Zoo is mostly that same junk you would find at any other gift shop. But is is one of my favorite zoo gift shops I have visited. This is because the gift shops includes the indoor exhibit for the African Spurred Tortoises, as well as a tank with a Siamese Fighting Fish. Sure, nothing out of the ordinary. But having, you know, actual animals in it does help. One more thing Racine has going for its gift shop is the fact that a good portion of the shop is devoted to painting done by the animals there. When I visited, I walked home with a painting done by the zoo's Fossa.
Another think about zoo gift shops is the setting. An gift shop that is filled with junk is better if it looks good. At Special Memories Zoo, the gift shop (while mostly stuffed animals that aren't even realistic



) does have some cool things, like ostrich eggs. It even has the the live animal going for it (a cage with a Patas Monkey). However, it is a garage attached to the owners house. It's very dark; the only light that comes in is through windows (small ones on the doors).
Another thing that infuriates me is when the stuffed animals in the gift shop don't match up with the animals in the collection. Menominee Park Zoo has a decent gift shop. No books, but the stuffed animal collection is nice, as most of it looks realistic. However, none of animals featured here are actually at the zoo!
As for the
best zoo gift shop I have ever seen, that goes to the International Crane Foundation. wonderful collection of (realistic) crane stuffed animals, very nice books for all ages (both fiction and nonfiction), and even some tabletop games (all of which relate to birds in some way).