I've never cried at a game, but when I shot Mordin in Mass Effect 3, I felt like ****. I regretted it pretty much instantly, and I think I came close to tears.
Also, although I can't quite remember, I have a feeling the ending to Red Dead: Redemption almost made me cry. --- "If there are two kinds of people I abhor most in life, it's egotists and hypocrites!" - Drophyd167b