I run ubuntu for my mythbox. My buddy, who is very excellent at Linux has looked into it. I own the nintendo four-score converted to USB
I don't exactly recall what the issue is, but from what I understand, each port returns 8bits (times 4 ports = 32 bit Human Interface Device)
What I think he's having issues with is for the four score to recognize that 8 bit boundary when you plug in a real controller. I've never dabbled with HID stuff in Linux. My buddy worked on it as best he could recording the logs and asking the usb game controller developer guy, but he never replied.
Thier single controllers probably would work, but I'm not sure. Sure as hell would be cool though.