Many other computer games allow you to point them at a folder full of MP3s and use them as background music for the game, allowing you control over your own soundtrack.
My suggestion would be - rather than just giving you the option of playing your own MP3s as background music, let you define themes for characters, events, etc. and then have the normal music algorithms use them instead of the built-in ones.
Helicopter sections: Airwolf Theme
Bombing runs: Ride of the Valkyries
Escaping on foot when it's all gone wrong: Benny Hill Theme
Original post on Dreamwidth - there are comments there.