wow, I had no idea some emulators could mute music tracks.  I'm pretty sure PJ64 doesn't, but does 1964?  They usually seem to have more features. 
I've actually found a program that extracts files from the roms themselves and converts them to wavs.  I've got all of Mario's "woohoo"s and a bunch of dying screams from Goldeneye.  Of course, along with the sound effects comes the instrument effects.  I can't extract from the Zeldas, though, because they use a different compression format.  Being able to mute tracks in-game would be awesome. 
These programs, Fast Tracker 2 and Mod Plug Tracker, can they export the notes as a file readable by sequencers?  Like, export into VST or anything? 
GOOD NEWS: I found out that the samples I took from SM64 are all in A4 already!   
So, if I want to use mario music, and I don't have a soft sampler, isn't it possible to create all the notes I want simply by making separate .wavs for each?  Like, I would take that A4 note and speed it up by 2^(n/12), right? 
*EDIT*actually, my ear isn't as good as I thought.  They might not be in A4...  Other than comparing the notes with a sin-generated tone(which isn't that accurate), is there any other way I can make sure?