You can hack a ps controller to your arcade controls and use it along with adaptors to play ps2, xbox and dc. Then you can hack some nes and controllers to your arcade controls as well. Only one system should be attached to the arcade controls at a time. My solution was to use molex connectors. When I switch systems, I have to unplug the current system and then plug the new one in.
I don't think I can recommend attaching an n64 to arcade controls. There just aren't enough games to take advantage of the arcade controls. I feel that they are best played on the original controller using the analog stick.