MK: Be Our Guest has one, but if you're looking for water fillups, nobody gets in there without waiting in line. There are no other refill stations in MK restaurants.
Epcot: Sunshine Seasons, Electric Umbrella
DHS: Backlot Express
AK: Restaurantosaurus
All resorts have them, but it appears that once the RFID filling stations go into effect, if you purchase a cup (a regular cup, not a mug) at the food court you will be limited to a certain number of refills (except for water.)