There's the Crystal Palace at MK with Pooh and Friends, they serve breakfast, lunch and dinner.
Liberty Tree Tavern at MK is Minnie, Goofy, Chip and Dale and I believe Pluto, they do a character dinner only.
There's the Garden Grill at Epcot. It's a revolving restaurant and they have Mickey, Chip and Dale and Pluto. I believe the character dining is for lunch and dinner.
There's the new breakfast at Hollywood and Vine at MGM. It's a character breakfast with the Little Einsteins and JoJo's Circus.
Those are the only ones I can think of off the top of my head that aren't princess related. I have two girls, so you can imagine where we always go
We took our boys to Crystal Palace for lunch in October and they loved it. My boys were ages 7 & 5 at the time. In fact, we are going back at the end of June when my younger son will be 6 (older son will still be 7). They said they liked it!
Ohana at Poly has character breakfast with Lilo and Stitch. My kids loved Stitch. He was throwing grapes at kids and genrally acting "bad". My son thought he was very funny.