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.
Phlegethon. 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!
Continuing the Crystal Tower quest and dungeons from Labyrinth of the Ancients, we now have Syrcus Tower. Besides being a massive shout-out to Final Fantasy III, it's another alliance raid, with the following four boss fights.
Scylla's fight is pretty much Phlegethon version 2. While she doesn't have any instant death attacks, and her Ancient Flare is toned down (assuming you stand in the puddles of water first), she solves this by having constantly respawning adds call Elder Staves that have various AOE patterns. Additionally, to even use the barrier mechanic for her AOE Stun and Damage Daybreak attack, players have to run orbs of electricity to terminals to power them up, while at the same time, freeing players hit with ice orbs using fire orbs, leading to a frantic fight with everyone constantly on the move. Scylla will also spam a dark version of Holy called Unholy, which comes with a deeper sound effect compared to the normal Holy used by White Mages.
Glasya Labolas requires the alliance to constantly stop various machines that are charging him up for a major AOE attack, as well as to redirect power to special pads that cause the players to jump away to safety. Players either have to have a member rush to Clockwork "Wrights" to have the power diverted to one player, while everyone else destroys the machine, or lure Clockwork "Knights" (based off of Final Fantasy XIII Pulse Machina soldier type machines) in between two terminals to redirect power.
Amon, is a mad scientist who dresses like Kefka with a touch of Kuja's music and theater themes to his attacks, such as Elemental Forte, and Curtain Call. Additionally, he calls various experiments of his to aid him in battle, while confounding the alliance by turning random members into Frogs, planting Pyrotechnic bombs on others that cause periodic explosions and knock away those near them, and tries to inflict Mini on others with special orbs. The alliance has to figure out how to turn these things back on their creator to help aid them to victory. Amon will also speak down to the alliance with polite mannerisms, viewing you and your party as "rude guests".
The final battle, is against Emperor Xande, the first ruler of the Allagan empire, who attempts to take out the alliance using powerful attacks like Ancient Quake, or by summoning multiple comets and a meteor. Xande even boasts how the stars must bend to his will.