Hi Jodi!

I love this question and I'm sure with so many great places to eat you will get lots of different opinions on this subject matter.
For breakfast my three top favorites are Captain Cook's Snack Co., Main Street Bakery and Sassagoula Floatworks and Food Factory.  Captain Cook's is located in the Polynesian resort and two words makes this a favorite of mine...TONGA TOASTt!  This is a Disney legend all of its own, bananas stuffed french toast deep fried and topped with cinnamon and sugar makes this a heavenly treat!  Main Street Bakery, located in Magic Kingdom, is known for its tasty pastries and the cinnamon rolls are definitively one of my family's favorites.  Main Street Bakery is closed right now and schedule to reopen this summer so in the mean time if you want to try the cinnamon rolls check out Gaston's Tavern.  Sassagoula is located at Port Orleans French Quarter so even if I'm not staying here I make the trek over to have some of their beignets.
 For lunch or dinner on  my top picks is Columbia Harbor House in Magic Kingdom.  The Lobster roll and clam chowder are very well done and there is seating upstairs that looks down on Fantasyland.  Restaurantosaurus in Animal Kingdom is also a great spot to grab a bite.   The themeing is fun and there are plenty of things for your eyes to explore.  My favorite dish here is the shrimp poboy, but they also serve burgers and sandwiches.  Tangerine Cafe is one of my top picks for Epcot, the portions here are really generous and I love being able to try different dishes from other countries.  Be on the lookout because you might end up doing some belly dances during this meal!    
Have a blast dining your way through Walt Disney World and we are always here to answer any of your questions.

Enjoy your delicious "Disney Time!"
Mandy