Ah, there are too many good ones.

Den of Woe, need I say more?

Mi'ihen, pretty much every possible outcome. My favorite has to be nabbing Rin as the culprit. "You're a jackass." "I will take that as a compliment."

Thunder Plains, it's the beginning of Brother and Cid making up.

Macalania Woods, that ending was well done. You really just wander around and recall the memories tied to it. There's no flashy scene or anything, it's all just quiet, like the woods always are. And slowly, they fade...

Bikanel, because it was really damn satisfying to finally kill Angra Mainyu. Also I love how you're rebuilding a sand barrier which you literally tore down in FFX.

Gagazet, Garik finally getting over his insane urge for revenge.

Coliseum (spoilers for the International version)Demonic Shinra is scary, but awesome. Also I'd really like to know what the hell is going on in Machina Panzer's ending.

I also like the fact that you can let genocide happen. And then you go round the world and not a single Guado is left. Quite sad.