This is a hard one to pick, because to me, it almost entirely depends on what kind of game it is. The type of game would determine that type of boss I would be and that would in turn determine what type of fight it would be and that would determine what kind of music would go with it. So there are many variables and there are many variations of music and boss types that I would want to do.
Anyway, that aside, I have always thought that this would make a great boss battle music. It's "The Real Man" from the Cowboy Bebop soundtrack. The way I imagine it in my head is it starts out with an intro cutscene leading into the fight, building up the tension and anticipation of the imminent battle. At around 1:05 is when the intro/lead-in ends and the actual fighting starts. (So if you are the impatient type and want to skip the cutscene, then jump to 1:05)
If the mood of the game called for a more classical feel, like a Castlevannia game or somthing like that, it would be cool to go with Schubert/Liszt "Erlkonig"
And just for kicks I'd like to give a shout out to TMNT Turtles in Time