I'm working on a plugin for ledspicer that will use the rpi GPIO pins, that means that if you are not using the GPIO port and want to hook some leds there that will be cheap and cool! I will post more details when I get a working version. As mitu mentioned you can use a led controller board to get the same (an a lot more) effects using ledspicer.

Software is ready to run my own game controller with dynamic lighting based on the emulator running at the time. Hardware is being built (waiting for some extra components). Created a project website for it :-p Retropie stuff Hardware schematics, software, photo's and video's will be posted ASAP. Greetings, ErX

Use python and it's native GPIO support :) But thank you for the link... So Arduino programs can be ported to RPi. You can usually use programms in the background to control switches even with ES running - because these programs are not "active" like in windows. They just wait for a trigger to act (=set interrupt)