Here what I konw of - maybe there are more...
Cosmic Ray's Starlight Cafe - Tomorrowland - Magic Kingdom
Seasons -The Land -Future World -Epcot
Liberty Inn - America - World Showcase - Epcot
Tusker House - Animal Kingdom
(cool - maybe fans, maybe no A/C, but was nice inside)
Restaurantosaurus - Animal Kingdom (McDonalds for lunch and dinner)
You could also go to the counter service of a deluxe resort - they are inside and have A/C such as:
Mara - Animal Kingdom Lodge
Beaches and Cream- Beach Club (small tables - gets very crowded)
Food and Fun Center - Contemporary (next door to a great game room)
Dolphin Fountain and Snack Shop - WDW Dolphin (fun 50's theme)
Gasparilla Grill and Games - Grand Floridia
Captain Cook's Snack Company - Polynesian (open 24 hours)
Roaring Fork - Wilderness Lodge