The only time I've ever cried was at the end on Xenosaga III: Also Sprach Zarathustra.
Spoilers Alert!
At the end when Jin and KOS-MOS die. He's the brother of one the main female protagonist Shion and she treats him horribly blaming him for the death of their parents. In my opinion he's the best male character in the game. If that wasn't enough the people at Namco-Bandai had to kill off KOS-MOS the Character who has been at the center of all three games and is focal point for the box art of all three games. That’s how the people at Namco-Bandai ended the series of Xenosaga ended by bumping off the main star. It is most satisfying end to a game I've ever seen in a game.
The following statement in red was a 100% sarcasm free statement.
I also cried at the end because Allan Ridgley got Shion Uzuki. I cried out from pure disgust. Pantywaists like him are not supposed to get the girl!
