Another toughie since I have only been 1 time and had all great experiences. Since I love pizza though I will say Via Napoli in Epcot was my favorite.
I love 'Ohana (I haven't been there in forever, and so happy I will be going back to eat there for New Year's Eve), Nine Dragons (Probably best Chinese food I've ever tried), for quick service it would be Yorkshire Country Fish Shop (I love me some fish & chips). There are plenty more but these are the ones that pop up in the head first.
I can narrow it down to my two favorites because they are a tie in my book. The 50's Prime Time Cafe and Boma.
I have ate at many great restaurants while at WDW, but my all time favorite is Be Our Guest. The Grey Stuff really is delicious. Don't believe me ask the dishes.