I just had this problem running a Lacie 160gb external drive (USB). It had been quite happy connecting to my iMac until I used it to back up some PC files, then it wouldn't boot on the Mac anymore.
First thoughts were that the drive had died and I'd have to take it back to the shop, but I firstly tried to connect it to a PC and it was visible no problem. So I then connected it back to the Mac, but this time I did so before switching the Mac on. Problem solved - the drive was visible again.
I can't be sure but I think the drive would hook up to the Mac before when the Mac had already been booted - I think the term is "hot swappable"? Try connecting the drive then booting the Mac, it may then appear on the desktop as expected.