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Tear Jerker: Suikoden V
The scene where Ferid and Arshtat die. Enough said.
Also, Ferid's last words, mouthed just before the Sun Rune obliterates him: "I love you".
If you get less than sixty Stars of Destiny, by the end of the game, Lyon succumbs to wounds she received earlier on and dies in the Prince's arms, as she tries to comfort him by saying that everything will finally be back to how they were before the war. By the time Georg makes his way to the scene, the Prince turns his back to Lyon's body, facing Georg and raising both his hands, showing that the Twilight Rune went from Lyon to him. He clenches his fists as though he wishes to crush the runes, tears rolling from his eyes, and Georg gives him a Cooldown Hug. Somewhat brief, but effective. The good ending(s) where she is resurrected by the Sun Rune is also a Tear Jerker in a good way.
When you see the scene of Lymsleia in Sol-Falena crying and wondering why the Prince didn't come back. Cut to the Arshtwal Mountains (or somewhere else equally cold and brutal), where the Prince is wandering. It's implied that he either left Falena to wander aimlessly in sort of a permanent Heroic BSOD - or that he simply wandered around in the mountains until he froze/starved to death.
What if someone takes up the Sun Rune again at any point in the future? Without the Dawn and Twilight Runes to control its power...
Once you realize what Sialeeds really has been up to after her Face-Heel Turn and her death, you would want to comfort her.
Roy's death scene if you choose the option to defend your castle.
Near the beginning, you have the Prince finding out the hard way You Can't Thwart Stage One and having to escape — including possibly being decked and dragged away by Lyon if he refuses to leave without his little sister.
When Lymsleia finally reunites with her brother. Rushing over to hug and crying for the first time since before her parents died and being forced into a sham marriage.
After the Godwin coup, the Prince is resting alone in his room at Lunas. He sits down on the floor, sad music starts to play, and he remembers his dad giving him big bear hugs, his mother's gentle encouragement, and Lym's cheerfulness, and now the first two are dead and the last one is held hostage. It's a bit of a downer until the Prince stands up, determined to fight.
Fail to meet the requirements for Lym's events being nice to her and it still becomes a downer in the end instead of the Prince standing up.