Living Seas at EPCOT is getting a Nemo redo. There's a sculpture outside the pavillion now with statues of lots of the fish in the movie and I've hear there are now tanks in the pavillion that feature characters from the movie (a "Nemo" tank full of clownfish, a "Dory" tank with blue tangs, etc.), but I didn't go in and see it when I was there. Nemo's also outisde the pavillion doing meet-and-greets.
I saw Brother Bear in Canada at the same location that TiggMan mentioned. They're also at Camp Minnie-Mickey at AK. No attractions yet. I wouldn't be suprised if they took out the Pocahontas show at AK and put in a Bear attraction there (would rather see that show get replaced that the Country Bears).
At MGM, be sure to visit Pizza Plannet. It's a Toy Story themed Pizza restaurant and it sounds like it would be a big hit with your son. The characters also do meet and greets at MGM. Buzz, Woody, and Jessie are usually at Al's Toy Barn, the Green Army Men can be found driving their van around the park, and Woody, Buzz, Jessie, Bo Peep, and the Army Men are in the afternoon parade. DisneyQuest at DTD also has a bunch of Toy Story themed attractions like Buzz Lightyear's AstroBlaster and Sid's Create-A-Toy. You may also want to visit the All Star Movies resort, which has larger than life statues of many of the characters from Toy Story. Great photo opertunities.