I was wondering, would there be any legal issues surrounding the use NSF, or music generated using FamiTracker in your own soundtracks for games? Or using Game Boy as an instrument as a part of your composition registered with ASCAP?

There are no legal issues surrounding music made with famitracker. The arrangement is yours, and the sound generation is entirely done using freeware/free software.

It only becomes a legal issue if you actually to decide to use soundtracks from existing NES games. Using DPCM samples from existing NES games is technically illegal as well. I don't expect that'll be an issue, but you can always avoid using those samples if you wanna stay safe. ;)

Oh yeah, that'd be like getting sued for using the presets on a keyboard you bought "those were our preset sawtooth waves! U CAN HAZ LAWSUIT"