It depends upon what you're interested in. If you want a good location for transportation, I would recommend staying at a monorail resort- either Ploynesian, Grand Floridian, or Contemporary. I've been to the Polynesian more than once and love the island atmosphere. Plus, not only is it on the Magic Kingdom monorail, but there is a walkway from the resort to the Transportation and Ticket Center, where you can board the Epcot monorail. (You can also take the Magic Kingdom monorail to the Transportation and Ticket Center, and get the Epcot monorail that way.) Staying at a monorail resort is a very cool experiance. The bus service has never been a problem for me at the Polynesian, Either. However, the themeing and decor are a bit old fashioned and not 100% perfect as it is one of the oldest WDW resorts.
For non-monorail resorts, many people claim the Wilderness lodge is the most beautiful. I've been there but never stayed there, though I have stayed at it's counterpart in California. Boat transportation is provided to the Magic Kingdom, but many have claimed that the bus service is bad because it makes too many stops at other resorts.
I've heard a lot of good things about the Animal Kingdom lodge. It is supposed to be beautiful, with good food, and amazing views of Disney's African savannah from the rooms. Plus, the bus service is direct, (or perhaps stops at Coronado Springs now). The only negative thing I have heard is from a friend who claimed it to be "out of the way" and thus that it takes a long time to get places via the busses.
Those would be my top choices (unless you really want boat transportation to Epcot and Disney Studios, which makes the choice more difficult, and I don't have much knowledge about the Boardwalk, or the Yaht Club or Beach Club resorts.)