Well, the first place you want to go is to City Hall - they have a huge print out that you can take of all of the gluten-free food at each restaurant or vendor in both parks. It was invaluable to me!
I loved that the Plaza Inn breakfast served gluten-free waffles (and they were really good), but hate that you have to pay character meal prices just to get them. Hungry Bear also offers GF buns for their burgers. Um, and that's about all that I can remember right now (rushing out the door to work), but the list is extensive.
I had a great meal at Tortilla Joe's in Downtown Disney too! Good luck, and make sure that you hit City Hall!