My neighbor had the same problem this week. Two different Nanos would show up on the Desktop but not in iTunes. An iPod Touch worked just fine. I, too, tried all of the normal things, to no avail. Since they were also seeing some weird problems with iPhoto (beachball requiring a Force Quit), I decided to pull out the big guns: I reinstalled.
I did a backup with Carbon Copy Cloner to make sure I had all of their info, booted with their Snow Leopard disk, used Disk Utiliy to erase the hard drive, installed, and used the Migration Assistant to restore the the CCC backup. It actually worked like a charm! Both Nanos and the Touch worked, and the beachball in iPhoto disappeared!
I'm sure I could have dug in and found some other problem to fix, but the reinstall was so easy that I figured there was no reason NOT to do it. And, given the results, I'd say I saved myself quite a bit of time trying to suss out the cause.
