Special mention needs to go to Answers, the main theme, linked here in live symphonic glory. The song is sung by Susan Calloway, the English vocalist from the Distant Worlds concert series, and Uematsu intended it for her from the start. The choral part is a complex layering of phrases and sentiments, and the lyrics manage to be both uplifting and heartbreaking at the same time.
And then... and then they set it to the end of Legacy. See directly below.
Could also count as a Tear Jerker toward the end. Even if you haven't played the game.
How about the Extended Trailer, A New Beginning? A True Masterpiece, indeed.
The boss fight with Titan. Ifrit, for all his flashiness, was a pushover. Titan? Is fought atop a platform so high up, falling off means instant death, out of reach of raise spells. He will occasionally target a random player with a knockback attack which may send them falling to their death. He will regularly use an attack which damages everyone in the party, which is a Difficulty Spike for a healer new to the fight. And twice throughout the fight, he will break off the edge of the arena, making it even smaller. All this, and he still has a One-Hit Kill move like Ifrit you have to interrupt to survive. How could this be any more awesome? With the rocking BGM that plays throughout the fight, getting more and more intense along with the fight itself.
And on the subject of Primal battles, Garuda's battle theme is something else.
EVERY SINGLE THING IN THE PRAETORIUM. From the Nero Tol Scaeva fight, even with his whinging about being in Cid's shadow, reuniting with your sentient Magitek Armor, Maggie, fighting Gaius van Balsar on a freight lift, and then fighting the ancient Allagan Superweapon, Ultima Weapon on another badass elevator reminiscent of the Olga Flow battle from PSO, seeing it use Ultima, confronting Lahabrea, good LORD what a finisher. And that's not even counting the extra lengthy and super-touching ending cutscenes!
"Escape From Castrum Centri". A rescue mission to recover the survivors of the Scions of the Seventh Dawn. Two fun fights, and a show of why the Scions deserve the respect they receive. Everyone shows their own form of Badassery, everyone gets hit with a major shock when they learn whose behind Lahabrea's mask, and the final escape by airship is one awesome moment after another.
The Labyrinth of the Ancients. It's the first dungeon to require an alliance of 24 players (3 parties of 8), and the bosses are designed with this in mind.
The Bone Dragon. It seems to go down pretty quick... then the skeleton enemies that you've been killing during the fight get back up and start running towards it. If they reach the dragon, the raid takes massive damage. Then the dragon gets up again. The fight isn't even half over.
Thanatos. He's incorporeal, so he can't normally be harmed. Good news, there are friendly NPCs who will turn you ghostly too so you can hurt him. Bad news, lots of enemies will spawn to kill them, so those who aren't ghostly need to protect them.
The Behemoth King. As soon as the fight starts, the floor becomes electrified. There is no safe place to stand. Instead, players are assigned to the four towers around the arena to keep them active, reducing the electric damage to manageable levels. Sometimes, a comet will land on a player. This is actually a good thing, because the Behemoth's strongest attack, Ecliptic Meteor, will outright kill anyone, unless they cower behind the comets left around the arena.
Acheron. The final boss of the labyrinth is actually not that difficult, but the mechanics involved are unlike anything else in the game, making for a very fun end to the instance. He has nonstandard shaped AOE moves, and the Ancient Flare, which will kill everyone unless enough people react correctly.
In the 2.2 story quests, the plan to defeat Leviathan in his own domain. Use a scaled-up version of the same tactic used to fly the Enterprise through Garuda's tempest. None of the Lominsan ships can carry enough crystals to make it work? Lash two ships together to carry them all! How is this thing going to get close to Leviathan in the first place? Tow it with another ship!