I tried SNES9x, and it doesn't appear to support mapping multiple buttons to the same input. Here's where things get tricky: I would like to be able to use both the analog stick (which is ideal for running around) and the D-pad (which is perfect for navigating menus) on the controller. Naturally I would prefer to use a controller rather than keyboard/mouse, so I grabbed my trusty 360 controller.
I was in the mood to play Chrono Trigger again and rather than put up with the disc loading times on my PS1 Final Fantasy Chronicles version, I figured I would just use an emulator.