So far, we've stayed at Shades of Green, Riverside, Coronado Springs, Polynesian, Swan, Dolphin and Wilderness Lodge.
I'd say my two faves are the Dolphin and the Wilderness Lodge, for completely different reasons.
I love the location of the Dolphin. With the Boardwalk at your backdoor, and being close enough to walk to MGM or Epcot, you really can't beat the locale. We also had a spectacular view of Epcot during our stay in February 2002 of Spaceship Earth and Illuminations...it was one of our best trips yet.
For theming, Wilderness Lodge wins hands down, IMHO, and was voted the #1 family resort by Travel and Leisure Magazine for a reason! It has such a warm and welcoming feel to it.