We all have difficult days and WDW can be an overwhelming, so tantrums do happen. You can minimize those tantrums by preparing your child for your trip in advance. Make him as familiar with Disney as you can before your trip: watch the animated movies, watch the free travel planning video, set your DVR to record Disney-related programs on the Travel Channel. Practice activities that your child will need to do during your vacation. Take him to restaurants where he'll have to wait patiently for his food. Go to places where you have to wait on some lines. Try to find some characters to interact with (maybe at a birthday party.)
You can head off many tantrums by making sure your son is comfortable. Is he hydrated? Hot? Hungry? Keep snacks, water bottles, and a portable fan on hand. Take breaks from the parks! Enjoy the pool at your resort. Make sure you keep to a schedule that is very close to what you do at home. It can be incredibly tempting to keep your kids up till 11:00 p.m. every night watching fireworks and seeing shows, but this will make your son a cranky mess. Save the late night entertainment for another trip.
I know that I get crabby when I'm in a long queue. Try to keep your son entertained while waiting in line. Keep a bag of diversions on hand: sticker books, silly putty, an iPod loading with a favorite film, handheld games. Also helpful can be giving your child some personal control over the situation. If he's getting cranky, let him pick the next ride.
I find that rewards are sometimes more effective than punishments. I'm not above bribery if it makes me have a happier vacation ;-). You could put a system in place that for each hour/day/etc. your son behaves (spell out in advance what this means so you're all on the same page), he can choose a souvenir (or earn points toward a souvenir) or a special activity.
And even with the best laid plans, tantrums will sometimes happen. In that case, you may have to have a "time out" in the theme park.