For those interested in using real retro controllers with Retroarch etc, I've adapted the gamecon driver to support Pi's GPIO. Currently, up to 4 NES/SNES/N64 pads can be connected to Pi (50mA current limit on 3.3V pin should be just enough for 4). I've tested the driver with 1st party SNES and N64 pads, but NES controllers should work too since they are similar to SNES.
My goal is to add support for PSX and multisystem joysticks at some point. There are also a few other joystick drivers in kernel, which could be adapted for Pi (or preferably for GPIO in general if possible).
The driver (source code, module built for 3.1.9+ kernel and instructions) can be downloaded here.