Speaking of crying...
The moment that always gets me is an Archive Log in the captured Quarian ship. Everyone in the ship is dead, and you find remnants of the logs to find clues of what caused the geth to re-animate and take control of the ship.
Then, I find a log. A Quarian woman shouts over the noise of geth weapons. "You have to be strong for Daddy! I love you very, very much!" Then, she's shot repeatedly.
Goddamn, the first time I saw that, I cried. I fucking bawled my eyes out