The funnel cakes at the cart in America (Epcot) are delicious. The pastries in France (Epcot) are really good.
If you are at Disney Quest, definitely get a cheesecake brownie. Soooo yummy.
Main Street Bakery at Magic Kingdom has a large variety of desserts to choose from.
Of course, the Dole Whips at the Magic Kingdom are to die for and I guess you could consider that a dessert even though it's not at a counter service type restaurant.
The apple pie at Aunt Polly's on Tom Sawyer Island is good.
I know I am forgetting a ton of them but I am sure that others will chime in.