Wow. Great advice everyone! I truly appreciate it.
I think you should run a separate game for him, probably using a simple system like Basic D&D or completely freeform
Well, yesterday after reading the first replies I decided to give this a whirl. I did make it simple and wanted to keep it more freeform. My oldest son (Gabe) likes having a book, character sheet, dice, mini, and battlemap since this is what he sees my group and I using. I use initiative cards that are basically distilled character sheets, so I printed off some and gave him one. Now, his 3 year old brother (Declan) wanted to play as well, so I set them both up.
I have some 3E PHBs, which look close enough to my 3.5 PHB, so I let them use those. I asked them both what they wanted to be when they played. I offered some suggestions, like being an elf, dwarf, or human and pointed out each one in the book. Both settled on human. Then I asked if they wanted to be a wizard, warrior, or sneaky guy (rogue). Gabe wanted to be a warrior and Declan said he would like to be a wizard.
Once this was decided, Gabe quickly flipped to the equipment pages and both he and his brother began choosing his weapons. We were just about done when Gabe stated to Declan, "You're a wizard! You need a wand!" So, I totally stole Abciximab's idea from his
Gaming with my daughter thread, and gave Declan's character a wand that could make things his friend or turn things into a frog. The only thing left now were names. Gabe chose "Swordy", which, by the way, is the name he uses when I let him sit at the table during my regular game. Declan decided he wanted to be called "Knight-Wizard", so I put their names on their character sheets and we were just about set. They both chose a mini, I gave them both 1 twenty sider and 1 six sider, and they were ready for adventure!
Now, I have to thank both Vorput for finding/linking and Abciximab for writing the
Gaming with my daughter thread because I stole not just the idea for the wand(s), but pretty much the entire story as well. I told them they were knights in the service of a beautiful queen and that some grumpy goblins stole the queen's fabulous unicorn and it was up to them, as brave knights, to find and rescue the unicorn.
It went by pretty quickly, but both boys were very very happy that they had such an adventure! As soon as it was over they wanted to go off to their toy room to reenact the whole thing! Now I'll have to make up something for another time or find more stuff to steal!

Maybe from Rel's
Samantha the Red story-hour (Thanks to Rel posting it and Xath for linking it) and Kirnon_Bhale's post (
here)
Once again, I thank you all for the great ideas! I think I'll have a way to keep the boys from going stir crazy during the upcoming winter weekends now!