There are just too many out there that I love, so I'm just going to name ones that comes to mind. There were a couple boss battle themes in Legend of Mana, they were spectactular. Heck, every boss battle theme that Yoko Shimamura worked on was great from Super Mario Rpg to Kingdom Hearts.
I like naming unique ones, because it's too easy to name Rpgs (Anything Final Fantasy was really good) For example, Capcom has always brought great boss battle music to the table in all their action games. Viewtiful Joe and Devil May Cry series set it up so that every boss had a different battle theme. My favorite in Viewtiful Joe's was in the first game when he fought a clone of himself. I believe it is called "Another Joe".