Another thing that's turned up on macintouch.com recently is resetting the firewire bus. You do this by disconnecting EVERYTHING from the computer, all cables, and the power. Let it sit for a while, like 5 minutes. Perhaps an hour or two wouldn't hurt. Then reconnect everything and see if there's any improvement.
Here's an Apple article on Firewire/USB problems: http://support.apple.com/kb/HT1317
That said, I have minis under my care with blown firewire ports, nonfunctioning ethernet ports--no bad USB ports yet, but I have seen it in the past on other computers. If none of these tips brings them back, then it usually means you need a new logic board.