Ive been doing a lot of research on this problem.
I tried a few things that did not work.
Tried another power supply. Still hum.
Tried attaching an electrolytic capacitor between +5V and GND pins on the GPIO. (This rebooted the Pi, (capacitor charging made a quick short circuit), dont suggest doing this while Pi is powered up, but I wanted to see if it made any difference while listening to the hum.): After rebooting the Pi, this didnt seem to help any at all.
I want to try a ferrite filter but couldnt find one in my junk box.
I tied a knot in the power cord between the power supply and the pi, this seemed to help some. (A knot in the cable makes a simple 60 HZ filter, although not a real good one.)
This humming problem does not exist when using the HDMI.
The hum is not really loud, and is not too bad if volume is not turned way up on the speakers (TV in my case).
I got my R-Pi NES case closed up, but I can easily take it back apart if I (or you) come up with any new ideas.