Wasn't there something about Quake always looking for the soundtrack in the first drive?
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That aside, yes, you could do that. Or you could use an engine that supports loading Vorbis or MP3 files. Or add that functionality to an engine.
or actually call the wav files from within the mod/map via sound/ambientsound entities - Quoth should have these... which doesn't help you if you need code, but Scourge of Armagon and Extras also have these entities I think.
The latter has the advantage of being able to trigger the sounds when needed instead of just playing a CD track. You can load pretty big wav files like this, although they must be mono (not that that matters much seeing as the game produces a lot of noise all the time anyway, not really audiophile listening conditions).
So there are different ways to have music in a Quake mod. In theory. I practice, I guess most ppl are going to want mp3 tracks or something.
I miss Doom midis and the sense of silliness they bring :p