Off the top of my head, air-conditioned CS include:
Cosmic Ray's at MK
Pecos Bill's at MK
Columbia Harbor House at MK
Pinocchio's Village Haus at MK
Main St Bakery at MK
Sunshine Seasons at Epcot
Electric Umbrella at Epcot (I never use this one, regardless - blech)
Lotus Blossom at Epcot/China
Liberty Inn at Epcot/US
Sommerfest at Epcot/Germany - not technically enclosed indoors, but located well under an overhang and received a/c from the Oktoberfest area so it's not hot under there
Tangerine Cafe at Epcot/Morocco
Yakitori House at Epcot/Japan - very, very limited seating indoors, though
Backlot Express at DHS
ABC Commissary at DHS (another one I never use, worst. CS. ever.)
Restaurantosaurus at AK
Pizzafari at AK