Mine is from FFVIII, called Force Your Way:

http://www.youtube.com/watch?v=E0kEe10l4cI

Are we talking generic boss music or "specific" boss music?

What do you mean by generic and specific?

Ughh such a hard question.
If I had to pick just ONE, then it's probably the final Cackletta battle them from Mario And Luigi Superstar Saga.

For instance; Final Fantasy 8.  That had boss music for most bosses, except Griever and Ultemicia both had their own music.

The Champion/Secret Boss theme from Pokemon Gold/Silver.

http://www.youtube.com/watch?v=2YodHq4iZFc

Hmm, does Clash on the Big Bridge (Final Fantasy V) count?

the 90+ songs of Xenoblade Chronicles hands down. Yo see more than 4 hours of beutiful and powerful soundtrack that mesh with the game, don't remember the boss batles but if you listen to the soundtrack u can find them. hehe sorry about tah.

Ah, I see.Well, either way is fine, as long as it´s really your favorite boss battle music in a JRPG.

I don´t know Clash on the Big Bridge, but if it´s music that plays during a boss battle, then yeah it counts.