I second the Museum of Natural Science. I loved the children's section, planetarium, Imax, dinosaurs, and butterfly garden as a child. Your kids might also enjoy running up and down the hill right next to it at the Miller Outdoor Theater.
A touch off the beaten path for family's (but still friendly), is going to the Orange Show, or the Beer Can House (both run by the Art Car people, I believe).
Oh, and paddle boats by the zoo.