Wilderness Lodge is our all time favorite. It just has an atmosphere like no place else. It's our true Disney "home"!
Animal Kingdom Lodge and Boardwalk Inn probably tie for second place. They are very different, of course, but we love them for different reasons!
Coronado Springs has the third place spot! (We rank it above some of the deluxe resorts we have stayed in - including the Poly and the Grand Floridian!)