We love Pecos Bill's in Frontierland for great burgers and fries. They have an excellent toppings bar with things like sauteed onions and mushrooms, cheddar cheese sauce, and the usual lettuce, tomato and pickles.
We also enjoy Columbia Harbour House for fish and chips and the like. Great atmosphere, especially if you seek out a table upstairs. It's hardly ever crowded up there; I guess people don't want to climb stairs with food and kids, etc. but it's worth it if it's not too inconvenient for you.
Casey's Corner on Main Street is your place if you're looking for a good hot dog. Fun, old fashioned baseball themed decor inside counter service with outside seating.