Oh, so many kickass boss musics... I can't determine an ultimate, but if I may name a few that rule?
Festival of Servants & Death Ballad from Castlevania: Symphony of the Night - The former is fast and vicious, and the latter is haunting and dramatic. Both fit in very well with one of my favorite games of all time.
Into the Dark Night from CV: Dawn of Sorrow - I felt rather excited when first hearing this, thinking A. "Wow, the DS has some awesome sound capabilities!" and B. "Now this is music made to fight by!"
Fortress Boss music from Contra - Even for an early NES game, the percussion in this one is impressive, and it generates such a dramatic an intense scene that's perfect for raging against the machine!
The Relic of Moirai from Contra: Shattered Soldier - Kurt says that Akira Yamaoka kicks ass, and for this music alone (and about half of the entire C:SS soundtrack), I believe him! (On a semi-relevant note, I REALLY need to play Silent Hill.
)
The original Gradius boss music - Such a simple tune that takes me back to some good days. It has been remixed countlessly, even if it really is only about thirty seconds without looping the track over. But I still like it a lot.
Roar of the Double Dragon from Double Dragon 2 - Even on the NES version, where the overall music quality takes a bit of a backstep from the first game, this tune just kicks ass. But OH MAN, the Arranged version (from the PC Engine version, I believe?) is perfect 80's-esque power rock that boils the blood.
Geese's music from Fatal Fury - It's been referred to by several different names, but no matter what game, big bad Geese's evil hard rock theme is one of the most distinctive in all of SNK history. Man, why did he have a different theme in Neowave, and why did it suck? Sacrilege!
Dear Falling Angel (Krizalid's theme) from King of Fighters 99 - I think that 99 and 2000 both have the greatest soundtracks from the series, but I may have to give my personal edge to 99 for this music solely. It seems like when the music explodes into the heavy guitar, Krizalid suddenly becomes a much more fierce fighter. That only happens about ten seconds into the fight, so prepare for an asswhuppin'!
Dancing Mad from Final Fantasy VI - What can you say about a music piece that comes in four parts, each one building up with more intensity than the one before it and culminating into a frightening final battle tune with Kefka himself? Not to mention that the battle itself is epic... we need more four-part final boss battles in games, I tells ya.
The Midnight Carnival from Guilty Gear XX - Fighting with I-No within a void of crimson skies is awesome enough, but with a kickass final battle music that rocks so hard it makes your senses bleed? Instant classic!
And finally, one that's not high-powered or fast-moving, but very unique and memorable:
The Stone Like from Radiant Silvergun - The entire orchestral music for RS all throughout has somehow been very fitting with the game, even if you'd be expecting more of a J-Rock or Techno theme. The music for the big confrontation with Xiga has no instruments whatsoever. It is entirely acapella, and is basically a chorus of voices harmonizing together. You'll just have to hear it for yourself, but going with the fact that you're fighting with a large red humanoid at the very end of time, it somehow manages to be one of the CREEPIEST freaking pieces of music ever. Mucho points for originality and disturbingness!
And as usual, I may add more later. ;D