Wow, thanks 1117, now I can't stop thinking about how to do this
With your permission I'd love to pick up an NES off eBay, do the mod with my CMoy, and post pictures (with credit going to you of course).
I'm thinking:
-Use the stock video and mono outputs as RCA input jacks.
-Use the original wall wart for power.
-Build an adapter cable to use one of the controller ports as a mini jack. (ie wire 3 of the controller port pins to the audio output on the CMoy, then splice a mini jack onto a controller cable).
-Use the controller for volume, power, and source switching. I'm thinking "select" will power off, "start" will power on through a relay. "A" and "B" can also go to a relay for source switching. The tough part is volume control with the d-pad. I think I would use my spare Arduino microcontroller board to take inputs from the d-pad and then rotate a servo-motor that is coupled with the potentiometer I'm currently using for volume control. Not too elegant, but simple and it will work.
EDIT: Doh! If I use the stock ports, I can only have one source. Maybe I could map A and B for power and leave start/select open.