Wolgang Puck's Express is, by far, the best counter service option available anywhere in Walt Disney World. Nothing else comes remotely close to this place. You get real plates, silverware, and glasses. A server actually brings out your food and dessert. But it is actually counter service. Weird, I know. And they don't use the standard desserts (chocolate cake, carrot cake, cheese cake).
Sunshine Seasons at Epcot is also really great, because of the large variety.
At Magic Kingdom, we like Columbia Harbor House, Cosmic Ray's, and the Main Street Bakery.
At Animal Kingdom, Flametree Barbeque is passable, and Yak & Yeti's counter service is good if you can find somewhere inside to eat (too hot outside!).
At Disney's Hollywood Studios, the only decent counter service I have found is at Starring Rolls. They have great sandwiches, and the desserts are made by the Brown Derby kitchen.