Don't know how many days you have - but I'd suggest concentrating on one park per day (two parks total), at least at first. The first day (DL) I'd shoot for Fantasyland at park opening, followed by Toontown once you've exhausted all the FL rides. The train ride around the park is always good for relaxing parental feet (if your son won't freak about the dinosaur panorama).
Don't forget Autopia in Tomorrowland - the only place in the world a kid can "drive" (with a parent along to push the pedal). That's one you can FastPass.
There is also a Buzz Lightyear show in Tomorrowland, and a Mickey's Detective School show in the Fantasyland Theater. When you enter the park grab a map for show times (or pick up a map at your hotel lobby, if they have them).
Early to mid-afternoon plan on the obligatory trek back to the hotel for naps (sometimes more for mom & dad than the kids). When you return to DL later you can rehit some of the favorite rides in FL and Towntoon, plan on a parade maybe, then trek back to the hotel for a good night's sleep.
On your 2nd day (DCA) there's the Redwood Challenge area, there's the boat by the McDonalds restaurant (name of the boat escapes me at the moment), there's also the jellyfish parachute kind of ride, and Flik's Fun Fair opens to the public 10/07 and is geared to the little ones.
Any additional days you have can be easily spent hopping back & forth between parks hitting the highlights your son likes most (focusing on Fantasyland/Toontown at park opening, then hopping to DCA later if desired)
