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Tear Jerker: Xenogears
This troper personally flat-out bawled during the entireending to Xenogears, especially since the song the plays through the ending (The Small of Two Pieces) is extremely heart-wrenching. However, it was more because "the game is over, and I've sort-of grown up with these characters and I'll never see them again," which can still be pretty sad, depending on who you are.
Yes. This troper hasn't played the game in years, but damn if that ending doesn't still choke him up. For the exact same reasons.
Xenogears has a tendency to dwell on scenes that more action-oriented games might gloss over, and thus make them tear-jerkers. One such scene is the attack on Nortune. There's plenty of material for action scenes, and, indeed, there is action. However, Fei and Elly look out on a city that is being consumed by flames, where ordinary people are suffering and dying. Later, Grahf narrowly saves Elly from death, and Fei's emotional response is a tear-jerker in itself.
Another scene is when Fei and Elly are shot down by Ramsus. It would be an ordinary setback in some other works, but the scene really drives home just how awful and heartbreaking the situation is:
Fei: Damn... The bleeding... The bleeding won't stop... If things don't change... At this rate Elly's not gonna make it...!
The scene in Xenogears when Fei flashes back to all the times when Elly sacrificed herself for him in all their previous lives is a powerful tear jerker, capped off with showing a distraught Lacan (an incarnation of Fei) turning into Grahf, driven to madness from his grief at losing Elly.
This troper manages to always tear up at the end of Xenogears. A combination of the mostly happy ending, the sad, sweet ending song, and the knowledge that the game is over is just too much.
Almost any of the flashbacks to 500 years before (especially if "The Treasure Which Cannot Be Stolen" is playing). Back then, Lacan, Sophia, Krelian, Roni, Rene, and Zephyr were a group of friends not so different from Fei and his companions. It's quite sad knowing how they were torn apart and what two of them became because of grief and despair.