MK: Cosmic Ray's, and it is delicious food, great variety and lots of seating. We ate there and loved it. Columbia Harbor House also has indoor seating but we did not eat there. I heard good things about it though. Not sure about other choices at MK but I am sure others will post.
Epcot: Tangierine Cafe had indoor seating. It was cool on a hot day.
DHS: Toy Story Pizza Planet had indoor seating but we chose to eat outside. It was not too hot (even though it was July) and we enjoyed it.
At AK I am not sure...we ate outdoors at Flame Tree BBQ.
I'm sure there are other places at the parks that have A/C and others will post!