All the music files are mp3 compatible.
Just go into the soundtrack folder, you can replace the songs directly, just make sure to make backups.
I know the combat music is 01001 to 01005, and the stuff above that I believe is the different sector musics.
Although it would be AWESOME to be able to add a separate folder for in-game music MP3s, and the in-game interface actually looks like a CD player!
I hope a dev reads this and puts it in a future patch. One thing that needs to be done other than this is to increase the amount of "transit" activities. To discourage people from using SETA, add ACTUAL afterburners back in, maybe script in a news service, that you can listen to in-flight, like NPR. You could give the code for it to the scripting/modding community, and they could do their own voiceover recordings, maybe add in video, you know, go hog-wild!
Ok, that's a bit crazy, but I definitely think a music tuner would be so cool!