Final Fantasy XII has quite a number of memorable boss battle themes. For the most part, there are six recurring boss fight themes, plus of course the final boss track. There are times when other tracks play during boss battles, but for now let's focus on those seven.
Boss Battle - This track plays for most regular boss fights throughout the game. As such it is probably the most well-remembered of all.
Clash of Swords - This track plays every now and then, most notably during the Bomb King and Mandragoras boss battles, and also on Pharos 3rd Ascent. It's quite different from the regular boss theme, helping those particular fights stick out.
Esper Battle - This track fittingly plays during every Esper battle. Very rhythmic and conveys the feeling of fighting a powerful mystical creature quite nicely.
Desperate Fight / Fight to the Death - This track plays during three story-heavy battles: Vossler, Cid I and Gabranth II. It also plays during one of the best superboss battles in the series. It particularly reminds me of the Judge Magisters, and how they really worked well as a group of antagonists.
Speechless Fight - This track plays during the fights with Ba'Gamnan, as well as the first Demon Wall. As such it's very nicely utilized first during battles you most likely want to run away from, and then again when you take your 'revenge' against those adversaries.
Clash on the Big Bridge - This track plays during the Gilgamesh encounters, and who could forget those? A very good remix of its Final Fantasy V iteration, playing during arguably the most memorable mark hunt in the game.
Battle for Freedom - Final boss music. I must say, Final Fantasy has always had pretty good final boss themes, and this one is no exception. However, unlike most others, this final boss theme feels very heroic, more like "this is our final battle and we will win!" rather than "this is the villain's last stand", in other words, more of a theme for the heroes than the antagonists. As such, it works wonderfully.
So, which of these seven is your favorite?
For me personally, it was a toss-up between Desperate Fight and Battle for Freedom, but I went with Desperate Fight. It's just that memorable. But well that's partially because of the Judge Magisters superboss battle in IZJS, which is one of the hardest and most epic fights I've ever had.