If it's lunch, and Be Our Guest is an option, then there's no question. That is far and away the premiere counter service option in the Magic Kingdom.
If you're looking for dinner, I think the best options are at Harbour House.
However, the flat breads at Pinnochio are delicious (particularly the caprese).
Cosmic Ray's is a glorified McDonalds.
I used to despise Pecos Bill, but in recent years they've added a lot of new options and greatly improved their menu. I love the tortilla taco salad because you can add whatever you want to it (they just give you the shell with beef in it).