I'm with lionheartkc - a little more info about your son's interests would be helpful! The most magical moments usually are somewhat unplanned, but you can increase your odds by doing things that involve activities or characters that are his favorites. A few possible examples based on other 6 year old boys I've run across:
If he loves Cars: head back to the area around Lights Motors Action first thing in the morning at DHS when Mater and Lightning first open for pictures - he can spend all the time he wants since there will most likely be no line when they open. He will probably also enjoy the Lights Motors Action show, so make sure to get in line early for a good seat.
If he loves pirates (either Jake or Jack ): If he's into costumes, spring for the Pirates League, and do it early in the day/trip so he can enjoy walking around in his pirate look. There's also the new interactive pirate game, and of course the POTC ride - if the characters are out for photos, which they should be while you're there, you can get some great ones of him in costume with them. If you really want to go all-out, you can spring for the Pirates and Pals cruise - especially if you don't live near water (and therefore he doesn't usually get a chance to be on a boat), that can be pretty magical.
If he loves Woody and Buzz: Make sure to get your Toy Story fastpass at DHS first thing in the morning - they go quick! But he'll probably want to ride it again, so make sure to leave plenty of time for that line again later in the day. Woody, Jessie, and Bullseye in various combinations often hang out in Frontierland, so make sure to go look for them there, and of course go on the Buzz Lightyear ride in Tomorrowland and meet him if he's over by Carousel of Progress while you're at MK. If he's into other Woody-like western things, you might also head over to Fort Wilderness some evening for the campfire - you can get there from MK pretty easily. He's probably a little young to appreciate Mickey's BBQ or the Hoop-de-do Revue, but if he is really into western stuff and has a long attention span and big appetite, consider those.
I hope that helps a little - again, with a few more specifics, I can give you more customized suggestions!