On our trip last August, we were in Satu'li Canteen for lunch when the skies opened. After eating and chilling for an hour or so, it calmed to a gentle sprinkle. We went from there to the Safari and had the best ride we've ever had. The animals were so active after the thunderstorm, even the lions.
Epcot - Mexican pavilion, Mitsukoshi in Japan
MK - Hall of Presidents, Monsters Inc, Country Bears etc.
DHS - Toy Story Mania, any indoor ride really