My favorite meal was at Jiko, at the Animal Kingdom Lodge. If you haven't already picked it up, you should get "Vegetarian Walt Disney World and Greater Orlando." It's a good reference book.
Anyway, I took the authors' advice, and I called Jiko to tell them in advance that I was a vegetarian. The chef personally called me two days later, and then emailed me a couple of dining options. I ended up getting something called, "Journey Through Africa," and the chef even came to our table to meet us and talk about the food. It was a great experience.
(Note - Jiko has a lot of vegetarian options on the menu. You don't need to call in advance, but it led to a really neat experience.)