My favorites are in this order:
The Boardwalk Inn and Villas - The rooms are clean (design-wise) and comfortable, and you can't beat the location. The Boardwalk also has some excellent dining and entertainment options right outside the back doors, and is arguably the only true rival to the Swan/Dolphin Hotels for that kind of variety on property. The pool, I think, looks like a lot of fun. I know people are creeped out by the giant clown head, but I find the concept of it hilarious. Think about it; who wouldn't want to watch a bunch of sunburned tourists be vomited out of a demented clown head all day? It's brilliant. Joking aside, the amenities at the Boardwalk surpass every other Disney hotel. There's a dance club, a dueling pianos bar, a sports bar, a signature restaurant that serves some of the best seafood on property, one of the best casual restaurants, one of the best bakeries, a laid back lounge, a fun pool with a huge water slide, a nightly carnival atmosphere on the actual boardwalk, a candy shop, a huge arcade... Seriously, the place has it all.
Animal Kingdom Lodge (Kidani and Jambo Houses) - The savannah view rooms offer one of the most unique hotel experiences in the country, at least in an urban environment. Sanaa and Jiko are two of the best Disney-owned restaurants, and they are easy walks from the hotels' respective lobbies. I've had some of my most relaxing post-park moments just chilling out with a drink from the Victoria Falls Lounge in the lobby, or just outside the back doors at the fire pit. The theming in both hotels is unrivaled, and the lengths they've gone through to obtain authentic art pieces to populate the lobbies is much appreciated. I could spend a week just scoping out all if the detail, and I plan on doing just that in November.
Port Orleans French Quarter - There are a few small reasons why I prefer the French Quarter side of this resort to the Riverside property. French Quarter and Riverside have similar bus service, in that they often share, but when they don't French Quarter's is light years better due to the size of the resort and there being only one stop. Even though they are smaller, I prefer the intimacy and inherently less hectic nature of both the lounge and food court in French Quarter. The big reason, though: size, in general. You can walk from one side to the other in French Quarter in less than ten minutes. There is no bad building, because none of them are ever very far from any one point of interest. The only real pluses that Riverside has on French Quarter are the pool and in-resort restaurant, both of which are accessible via five minute walk from French Quarter, which is still a shorter distance than some people need to walk within the resort to get to the feature pool in the other moderates. Throw in the boat transportation to Downtown Disney, and I think French Quarter is the winner out of that price class.
Wilderness Lodge - As far as hotel theming is concerned, aside from the aforementioned Animal Kingdom Lodge, I don't think there's another hotel on property that has so perfectly committed to the story behind the architecture. It's all dark woods and lofty, echoing ceilings. There are large fireplaces, rocking chairs and small stream running through the middle of the lobby. As an added bonus, if you're there during the holidays, it is easily the most amazingly decorated hotel on Disney property. And then there's Artist Point, which at certain times of the year, depending on the game and fish available, can a top three dining establishment. Last time we ate there, the menu was amazing. Two words: venison carpaccio.
Contemporary - Now, I've never actually stayed at the Contemporary, but out of all of the monorail hotels this is the one I want to stay in most. I love all of the restaurants and lounges contained therein, and it's walking distance to the Magic Kingdom. Ever since I was a kid, I've always been intrigued by the sleek design and cavernous innards. It's like being inside of a hollow mountain. Being able to wake up there everyday on a trip would be a little bit of awesome.