My 3 year old's favorites:
Ohana (he calls it the coconut hula hoop place)
Chef Mickey's (great character interaction)
Crystal Palace (Pooh breakfast)
Sci Fi (loves eating in the car with the big TV)
Pizza Planet (he loves Toy Story)
Restaurantasaurus (loves dinosaur puppets in the happy meals)
Coral Reef (eating with the fishies)
San Angel Inn (he callis it eating with the mountain)
Cosmic Ray's (he calls it the singing dinosaur)
But we take our kids everywhere. Disney is very kid friendly at all the different restaurants.

Even our 1 year old can sit through a meal.

The only place we ever had a problem was Concourse Steakhouse, and I think it was mostly due to them being overly tired. A good piece of advice, if you have a favorite "nice" restaurant (ours is Palio's) make a PS for 5:00 pm. That way you can eat the food you love and your kids don't disturb the romantic couples that eat later.

We always notice more younger kids at the earlier times.
