At Magic Kingdom I love Cosmic Ray's. The portions are huge and they have a great fixings bar (I believe Pinnochio's and Pecos Bill's has this as well). I also really like Columbia Harbor House because it's different from other counter service restaurants. The tuna salad and ham with broccoli slaw sandwiches are great! And as one of the previous posters said, eat upstairs. It's way less crowded and there is a bathroom up there that no one uses.
As for Hollywood Studios, I've only eaten at Pizza Planet and ABC Commissary. Both we're fine.