I hope you don't mind several, because I can't pick just one.
It's fitting that a Final Fantasy game that doesn't fit in with the way Final Fantasys usually are has boss music that feels more... Capcom<?> in a way than Square, but this one rocks.
Can't have old school Square without having Enix, so here we go:
7th Saga was certainly a game that liked to kick your ass. Whenever this theme played you knew you were likely going to be in for a brutal fight.
Taking a break from RPGs for a moment, fighting games can have some pretty hot jams too.
Samurai Shodown 2's "Wicked Heart" for the Mizuki fight gets my blood pumping.
I'm also a fan of some of the boss themes from the Battle Arena Toshinden series:
Can't pass up "Full Bore" which is Fulgore's theme in Killer Instinct:
Switching back to RPGs
This is the music to which Cynthia taught me that my best was simply not enough. Beating her felt like WORK.
Breath of Fire is one of my favorite non-FF RPG series, and I remember searching forever for this song as soon as I had the capability of looking:
Both III and IV deserve re-releases on modern consoles:
I remember this track mostly from the phoenix fire druid fight in WoW, but it may have played elsewhere?
And lastly, because I promised myself I'd only post one FF XIV song:
It's not THE Alexander boss theme, but it is SO GOOD.
