I can't say i ever "cried" playing/watching a video game , but i had "misty" eyes numerous times during the Metal Gear series, especially in some specific scenes of MGS4 and 3.
I cried like a baby however, when i watched the animation Grave of the Fireflies. It was an incredibly emotional experience and the fact that it was inspired by the true story of a brother and sister, was even more heart breaking.
"You have the right to the remains of a silent attorney"