Any of the character meals are, of course, great for little ones. Some of the others I would consider fun for kids are:
Biergarten in Germany, Epcot- they have an oompah band that plays, and kids can get up and dance on the dance floor in front of the stage. DD loved doing the Chicken Dance. Food is also pretty good- nothing weird or spicy.
Marrakesh in Morocco, Epcot- The kids' menu has "normal" food, and there is a band that plays Moroccan music and a belly dancer.
Teppenyaki in Japan, Epcot- If you get a good chef, they can put on quite a show. It's a Benihana-cook-at-the-table style restaurant.
Coral Reef, Living Seas, Epcot- fun for kids who like to watch the fish in the big tanks.
Sci Fi, MGM- The restaurant looks like a drive-in theater, and you sit in old convertibles and watch silly old 50's sci fi clips on the big screen.
50's Prime Time, MGM- Mom's kitchen in the 50's setting, and the servers get into character, telling you to eat your veggies, etc. Especially fun if you are the type that likes to play along with the antics.
Rainforest Cafe, DTD and AK- not on the Dining plan, but fun. Rianforest theme complete with storms, animal noises, etc.
'Ohana dinner at the Poly- Hula hooping, coconut races, and Hawaiian singing- and good food. If you are there late, you can see Wishes from the windows.
Whispering Canyon Cafe, WL- The servers really like to play here- ask for a LARGE drink, a straw, or some catsup and see what happens!