hmmm, interesting idea. xbox controllers would be the easiest, as they are already usb. but to find a small enough controller to hack that could fit into a sega controller, let alone a nes controller...
but what about a pc controller...if you limited yourself to a single analog joystick design, you could probably get a really small controller for the pc, but then you could only play games up to n64 and the equivalent. as for paddle controls, i don't know what you'd do for that.