Well, I can't say it's my favorite (there are several that fit that description) but I just tried Columbia Harbour House for the first time and was very impressed! The food was very good and fresh tasting and we sat upstairs (it was empty!) over the walkway outside HM and had a ball people-watching!
I love Flametree BBQ at AK, Sunshine Seasons at Epcot, and Pinocchio's Village Haus at MK.
the food court at por! we ate there 3 times over our 9 days and the pasta was great! it was great to send my dh for dinners to go so we could watch football while eating dinner....we believe in relaxing while at wdw.