The opening FMV of FFX-2.

KIDDING.

Let's see, so many...

Super Metroid - The final battle against Mother Brain. Fans of the game know what I mean.

Metroid Prime 2 - Battle against Quadraxis (both the music and the enemy are so epic), and the very end when Samus gives a little back hand wave to the Luminoth. She kicks ass.

Chrono Trigger - The whole game.

Chrono Cross - The aforementioned scene with Miguel in the Dead Sea, also when you go back in time and (SPOILER)rescue Kid from Lucca's burning orphanage. Also, Kid's words at the Water Dragon Isle around the campfire. That song gets me every time.

FFI - I'm weird, I know, but something about the entire game appeals to me. It's quaint.

FFVII - The very very end, after the credits, where (SPOILER)Nanaki and his apparent children look out over the ruins of Midgar. Probably one of my favorite scenes of all time. I also like the scenes in the Shinra building involving Jenova. There are a couple songs there I enjoy. Plus, any other scenes folks have mentioned.

FFVIII - All the FMVs. I don't know why, but they have always resonated with me.

FFIX - Kuja's appearance, all scenes involving Eidolons, the ending.

FFX - The sending at Kilika, the scene at Home, the scene with Yunalesca, the ending. They've all been said.

FFXII - While I find the entire game beautiful and memorable, my favorite scene is probably the one at the top of the Pharos at Ridorana, especially the tidbit involving Balthier and Fran. And the ending, of course.