Heh, he took the easy way out and put USB inputs next to the old controller ports. I've seen people go as far as to rewire their keyboard and mouse to find inside the NES controller ports and wire that to the motherboard. There used to be a site dedicated to NES PCs called junk-machine.com, but it looks like it's gone now. I haven't checked the site since 2004, so I dunno when the site was canned. Too bad, that was a really cool site.
I remember I really, really wanted to do this when I was 15. Funny thing is that I didn't know anything about building computers back then. I'd probably be able to do it now, if I had the patience and soldering skills which I seem to have lost.