My son just upgraded from a Suzuki OR50 which is actually a 50 cc 5 speed small motorcycle. He learned how to shift on this, didn't take him long and this bike tops out at about 60 mph.
He is 17 and about 6 feet tall and thin so we started looking at Honda Rebels (used). Like Ike said, you can get brand new ones for $2999. They come in a 250 cc and also a few 450 CCs around. He (we) agreed that he would probably outgrow the 250 cc pretty quickly but I didn't want him to get too much bike. So we were considering a Honda ? something under 500 cc.
In our research we lucked out and found a 1989 Honda Shadow VT600 VLX for about $1000. Blue Book is around $2800. The previous owner had a fender bender on it and scared the pee waden out of him I guess so he doesn't want to ride anymore. The only damage was a broken turn signal, bent handle bars and a few scratches on the chrome. Forks and wheels were straight.
Since my son learned to wrench on all these mopeds and ride and shift his Suzuki he is ready to tackle a bigger bike. He has also made friends with the local Honda dealer mechanic and is using the public library for Service and Repair manuals.
He is going to CC-Riders Basic Riders training school (this is required to get a M1 license if you are under 21).
As a Dad I am concerned about him riding a bigger bike but he is a good rider, safe and rides defensively.
So I would say check out the used Honda Bikes Matt. Try www.CycleTraders.com, Yahoo classifieds and your local paper and of course EBay.
Here are a couple of good links to educate yourself before you decide.
Good Luck and Happy Trails