For me, the best memorable scene would definitely be in Star Ocean 3, when Dion and Ameena died about 5 seconds apart from eachother. It was sad. I really liked all of the scenes in that game, and one of the reasons is because of the wonderful background and scenery graphics.

In Kingdom Hearts, when I first saw the ending I cried. It really touched me. I also cried for the ending of CoM and KH2. And when Aeris died in FF7. I cry a lot for games. Nothing else.