MGS4 last fight between Snake and Ocelot.

There are way more boss themes I love, but those have already been mentioned.

EDIT: Added one more.

Xizan from Guardian's Crusade



Xemnas from KH 2

Arc Rise Fantasia's "Unexpected Battle", such an amazing and pumping piece of music. "Before the mighty one" from the same game is also wonderful.

Pokemon XD's Cipher Admin theme (it also plays with the leader of each area in Mt. Battle). Amazing! Also Greevil's theme is so good as well.

Anything on Monster Hunter 3 Ultimate, specially the second Jhen Mohran theme, "Intercepting The Great Gong". Beautiful composition, the strings are no joke.

Megaman X Command Mission, "Rebellion Cadre Theme", dramatic, I love it.

I've always liked ZUN's music in Touhou Project. And of those games, I'd say the boss music for Flandre and Okuu are two of my favorites, the latter's theme sounding more boss-like of the two in my opinion.