(SPOILER)Gaignun's sacrifice at the end of Xenosaga, as well as Albedo going to sleep all tore me apart, as well as seeing chaos dissapear and KOSMOS' torn apart body floating in space- all from Xenosaga.

Vivi from FFIX was also a heartwrencher.

EDIT: I just read a post with Lavitz from LOD. As cool as "The Platinum Shadow" was, him killing my favorite Dragoon was just unbearable.