Well I finally got my original guncon2 and hooked it up via composite by way of the svideo-composite adaptor that came with my card. Any how quick test says it work pretty decent, tracjing was jerky probably cause it was black and white, couldn't seem to get color with the composite adaptor. Also like others it seems to not track at all on about 3 inches of the left side of the screen no matter what the resolution (640X480 or 800X600). Also only button A seems to register (as button B) in the little test application, no other buttons register at all. And for the record I have a trackball hooked up via the ps2 mouse port, a spinner via mouse via usb, and the guncon2 via usb (all three still work).
Anyhow I definately think it has potential. Also I'm going to hack an s-video like brandon did and give that a go, then later try out the component video on my other video card...