I have several favorites based on different criteria.
Favorite table service food: Le Cellier - a Canadian steakhouse in the Canadian part of Epcot's World Showcase.
Favorite counter service food (and very reasonably priced, for Disney): Earl of Sandwich - the sandwiches are delicious (their bread is so good), and their sides and desserts are, too. Really packed around lunchtime, but the line moves fast.
Favorite theming: probably Sci-Fi Dine-in - a table service restaurant in Hollywood Studios - you really feel like you're in an old drive in theater when you walk in. You even eat in cars, and watch old (and I do mean old) sci-fi flicks.
Favorite service: the Rose and Crown - a table service restaurant in the England part of Epcot's World Showcase. We really clicked with the waitress one year there, and they named us "family of the day" and gave us free smoothies, party hats, fussed over us, and otherwise treated us special. It was just one of those "magic moments."
Favorite dessert: the Chocolate Wave at Epcot's Coral Reef restaurant in Future World (a few years ago... the more recent versions are nothing like what that first one was.) Oh my goodness... every chocolate dessert pales in comparison. I wish they still made them like that first one.
These favorites are based on when they had a good free dining plan. Now I wouldn't spend the money on any of them except for Earl of Sandwich (which I visit every year). The food at the off-property restuarants is better. (The taste and quality of the food at Disney restaurants has gone down due to the free dining.)
What are your favorites?