In reply to BradLTL:
If travel time is flexible, I'd strongly advise the first two weeks of September. Crowds will be minimal, ride waits will be nonexistant (excepting headliners), it will be hot as all get out, but the heat is worth it for the low crowds. You also have an excellent chance of scoring free dining, which, if you're planning on character meals, will be a huge value. Utilizing free dining will require than you buy a 'package' through Disney, which can negate some of the savings, but for character meals, it's worth it to me.
For Fastpasses with a 4-year old, I would make sure to grab Seven Dwarfs Mine Train (it's a calm coaster and very cute), Peter Pan's Flight and Pirates (be warned, theres a blind drop in Pirates where the ride goes under the railroad that encircles the park. You'll know it's coming because everything will go pitch black) in the Magic Kingdom. For EPCOT, Soarin' is amazing and really only rideable with a FastPass unless you want to wait in line for an hour or more, Turtle Talk would be my other must grab here, the Character Spot. For HollyWood Studios, Toy Story Mania is another 'only do with a FastPass' ride, waits here can be upwards up 2 hours even in low crowds; followed by Star Tours and Great Movie Ride. Animal Kingdom is a strange beast with a kid that small, so use your FastPasses for Kilimajaro Safaris, Festival of the Lion King and Finding Nemo the Musical.
Schedule your FastPasses early in the day. Making them early will allow you to go to a kiosk and schedule a fourth. In EPCOT, use the fourth for Test Track and in the other parks use it for something that was a favorite previously.
Getting back to Character Meals, schedule pre-park opening breakfasts in every park that you can except Hollywood Studios. Reservations open 180 days out, and the early ones are the first to go because they come with a BIG perk: You get into the park before it opens and get pictures from the PhotoPass Photographers with a practically empty park behind you. Favorite character meals for our trip were Chrystal Palace in Magic Kingdom (a buffet with Winnie the Pooh, Eeyore, Piglet and Tigger, and the only place in the park to get puffed french toast, YUM), Garden Grill in EPCOT, which is only open for dinner (Mickey, Pluto and Chip 'n Dale), fun fact, a lot of the food served at GG is grown on Disney property, and it is delicious. I don't eat steak at all, I did here. In Animal Kingdom, Tusker House breakfast buffet is great (Donald, Daisy, Mickey and Goofy, although there are rumors Goofy has been needed somewhere else in the morning). Hollywood Studios is a bit different in that my priority here is the Fantasmic Dinner Package more than a character meal. The Dinner Package doesn't cost you any more than a regular meal/single sit-down credit, but you eat at an earlier time and get reserved seating for Fantasmic, which means you don't have to be in line 2 hours before the show starts and the 'Fantasmic theatre is at capacity' announcements do not apply to you. You can walk into the theatre 15 minutes before showtime and still get an amazing seat (we were 4 rows back and had no one next to us). If Fantasmic is not something you are planning to do, then Hollywood and Vine has Disney Jr characters and good food.
We're not planning a trip for this year (even though I wish we were) so I haven't paid attention to the free dining rumors, but typically Moderate and above give you the regular dining plan which is one sit-down, one counter service and one snack/night you're there, which is a lot of food. The counter service meals are NOT split by child/adult, either, so you could maximize the value by ordering 2 adult meals and sharing with your son. Table service will cost you for each person dining, though.
Also, since he loves trains, make sure you hit the People Mover in Magic Kingdom, it's a 'train of the future' and gets an inside view of several Tomorrowland rides and some of Walt's original models for the parks, which are like little towns for a train set. There's also a huge train set in Germany in EPCOT what is mesmerizing to watch for a while.
OK, I think that's all the big points, or at least enough of a brain dump for now. Let me know if you have questions about anything :)