LOL at knittingforums.com. It's important to maintain a sense of humour under adversity
I was half-way through mentally composing the "have you flashed your BIOS?" response when I read your last sentence. In a way, I think it's important that you overcome the USB device side issue because flashing the BIOS is an important step in these situations. The BIOS code controls much of the hardware-level power management and power state functionality, and bugs in the BIOS can easily manifest themselves in this way.
Otherwise, you might want to rip out as much non-essential hardware and then test again. Remove the mouse, all expansion boards you don't absolutely need to run the box, all HDDs except the boot/system partitions, all USB/firewire-connected devices... The point is to test whether the smallest-possible hardware configuration does the same thing. If not, then you start adding things one-by-one until the symptom comes back.