I have a PC, and a DS3 controller. I have the driver to make the controller work on the PC. I started the rom that I wanted to play, paused it, went into Input>Joypad configuration. I went through each button on the snes controller, pressed the buttons on the PS3 controller that I wanted each one to be linked to, hit ok at the end. I went back to the game, but whenever I hit any button when prompted to choose 'start' or 'options' in the game nothing happened. The controller works on my mame emulator, so does anyone know why it's not working on my snes9x?

Its probably because you need to configure it before you start a rom on the emulator. But each emulator is different. I've always configured my PS3 controller before I started any rom. So far it hasn't let me down. I've used it on both snes9x and zsnes, works fine for me. Give that a try. Hope it helps.