I don't generally think of counter service restaurants as "fun," but if you are lucky enough to get a table near the window into Small World in Pinocchio Village Haus, your kids might enjoy watching the Small World boat loading area. Plus it's cutely themed.
Cosmic Rays has an audio-animatronic alien lounge singer.
In Hollywood Studios, Pizza Planet has Toy Story theming and is actually also an arcade (but if you don't want your kids asking for money to play the arcade games, you may want to avoid it).
In Epcot, the Sunshine Seasons food court at least used to have some child "chef" activities. I have no clue if they do anymore though.
In Animal Kingdom, Pizzafari has the most "fun" theming, but Flametree BBQ has outdoor seating, some of it down near the water which can be fun to look at.