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Tear Jerker: Jade Empire
Jade Empire, the most recent of BioWare's games to include a Good and Evil Karma Meter, left this troper heartbroken when he found out he could spiritually enslave Death's Hand. Then, when his party objected, he spiritually enslaved them. And you can steal the power of the Water Dragon. You will never feel so bad for doing anything else in a videogame.
There is a mission wherein a doctor is trying to find a fresh corpse in a graveyard to replace his daughter's dying organs with. The player character finds an Undead by the name of Ji Xin who preserved his corpse out of fear of the afterlife because he knew he was fated for damnation due to all his sins. The player can simply kill him for his organs, but if you persuade him, he gives this heart wrenching line, "For a little girl? Yes, very well. If Damnation is my fate, at least let it be worth something in the end."
Wild Flower is the personification of a tearjerk moment. She is a poor girl who died during the flood in Tien's Landing and who now has the souls of two rival spirits dwelling inside her and warring over possession of her body. Her innocent struggle with them and her painfully sad fear of the bad spirit could make a statue cry.
Miss Chan's fate in the Necropolis quest. Not only did she die in childbirth, but her baby died along with her, and she's understandably unable to accept that fact.