Some of mine:

The death of Aeris

Xenogears - Fei turning into ID and raping that flying city

The sword fight at the beginning of FFVIII

Bahamut Vs. Alexander in FFIX

Yuna performing the sending in Kilika at the start of the game. And the ending.

The ending conversation between Snake and Otacon in MGS 2 regarding the Patriots

The final battle in MGS3 in the field of flowers, especially when the Snake Eater them begins to play + the narration that followed + the salute.

The return to Shadow Moses in MGS4, the microwave corridor, Snake Vs. Ocelot

In Heavenly Sword, the Kai and Flying Fox scene with Nariko screaming for Kai

Valkyria Chronicles, that one scene with the Main Character's sister followed up by Rosie singing