Knuckles didn't write this emulator. Also, it is well known (and documented) that only 1 controller works. Just be patient (based on what I've read, wait about a year, or 3), and I'm sure that they'll get more controllers supported eventually. In fact, if we're really lucky, they might even enable multiplayer online (sort of like Kalaira, or however you spell that thing for other emulators that provides online access [it sends controller data to the other emus, or something]).
Though I haven't tried this emulator (or any GC emus, for that matter), I think I may give it a try. I like emus because, especially with these new 3D ones (depending on the improvements they've recieved), you can get high-res in-game screenshots. That's what I want them for. I plan on running Skies of Arcadia (though it will almost certainly not have sound. The music is sequenced (like midis) and those aren't supported yet, that I've heard. Streamed media (like MP3 or WAV) is what you're hearing, when a game has sound in these emus) to see if I can get any pictures from it. I might also run PSO 1&2, and maybe even PSO ep. III.
Anyway, the comments are mostly all good. Hopefully, I can get this doing what I want it to... Mouser X over and out.