Final Fantasy VI
Ladies and gentlemen, I present the granddaddy of all Final Battle themes. One Winged Angel was a phenomenon, but Dancing Mad will probably never be topped.
Of all the great RPG's I've played, Final Fantasy VI feels the most epic. 'Epic' is a word you see thrown willy-nilly around the internet these days, but when I invoke it here I am using its classic meaning: grand and deep both in scope and impact; a long, involved and life-altering journey. By that definition, no game's story carries the weight Final Fantasy VI's does. And it all culminates with--and I mean this both in the classic sense and the internet sense--an epic final battle accompanied by epic music.
I think the second-longest piece on this list, not counting loops, is yet to come; it's about five and a half minutes long. Dancing Mad is three times that length, or about twice that length if you discount the fact each of the first three movements is played through twice.
Which brings me to my next item: This music comes in four distinct movements, which you will see called 'tiers' since they correspond to the four tiers of your fight against Kefka. Each has its own distinct flavor: the Face/Arms tier is menacing, the Four Parts tier is relentless and oppressive, the Hit/Girl tier is dark and spiritual, and the Kefka tier is powerful, out of control and insane. All the music falls into place. This is the closest thing to a bona fide symphony video game composers have ever assembled. Listened to in whole, the effect is tremendously impressive. Like Final Fantasy VI.
Consider the general story flow of Final Fantasy VI. You start out as the loosely-defined leaders of an underground resistance against the Evil Empire (yes, they're just called the Empire) led by Emperor Gestahl, who is swiftly and bloodily conquering the world with Magitek, machines infused with magic power drained from Espers, mythical creatures made of magic. Against Magitek no army has a prayer of standing. Gestahl is supported by three powerful generals who are kind of aligned against each other on the Magitek spectrum: Leo, Honorable Warrior Extraordinaire who refused to be infused with magic; Kefka, who happily accepted the magic transfusion but went semi-crazy and started dressing like a clown and generally became a very loose cannon; and Celes, who wasn't given the option but instead was infused with magic as a very small child, and who eventually goes rogue and joins/arguably takes leadership of the resistance.
I mean, right there, even if you'd never heard it before, you'd have to agree that's a hell of a basis for an epic story, right?
And so it is. Your Returners spend the first half of the game struggling against the Empire--and making use of Espers and magic themselves in doing so--and generally finding mixed success. But Gestahl proves a very wily opponent indeed, and successfully tricks the Returners into walking into an ambush right in his own capital city, resulting in the slaughter of pretty much all of them except your party of PCs. After which Gestahl reaches his ultimate goal: meddling with the statues of the three goddesses that created the world, the source of the very power of creation.
At which point a monkey wrench gets thrown into Gestahl's grandiose plan: Turns out Kefka had world domination plans of his own and Gestahl doesn't fit into them. And it also turns out Kefka has been studying. He knows a lot more about the Statues than Gestahl does. As soon as they find said Statues, and just as your party arrives to try to save the day, Kefka whacks Gestahl, tosses his dying body off the Floating Continent a couple miles up in the sky, and starts moving the Statues around. Which results in ripping the world apart and rearranging it pretty much at random.
You can guess why the rest of the game is called the World of Ruin.
So you flash forward a year, and then spend the rest of the game, starting with Celes, reassembling your party that was scattered to the winds to form one desperate assault on Kefka, who now is both certifiably insane and a god. Literally. Most Big Bads think they're gods or aspire to be gods, but this is the only game other than the Lufia games I know of where you are actually expected to fight and defeat a god.
So anything less than truly epic music to accompany your battle against a god would be disappointing. Final Fantasy VI does not disappoint.