There's a cool feature in VisualBoyAdvance that let's you pick and choose which of the four sound channels are playing at any time; very useful if you're trying to learn a particular bass line or harmony on an actual instrument. Are there any NES emulators with a similar feature? I use RockNESX and it does not.
I don't play around with NES emulators often, but there are lots of music players that let you disable sound channels for tracks. The two that come to mind at first are Nezplug and Audio Overload. Those players only wrk with nsf files, though (which you could download from here.