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Tear Jerker: The Legend of Zelda Oracle games
That annoying guy who's been pestering you throughout Oracle of Ages is revealed to be the future descendent of the possessed queen... and he is prepared to kill his own ancestor, erasing his own existence, if that's what it will take to stop the Big Bad.
Ralph: Fine! If I slay you, I vanish! Maybe it is terrifying... But if I must, I must. To do nothing and live just isn't me.
The reunion of Ambi and her lost lover, the Pirate Captain in a linked game of Oracle of Seasons.
The grandma whose grandson has been tuned to stone.
The pirate ghost who goes to heaven after finding the bell. Of course, you find out later he got stuck halfway, apparently having forgotten how to get there.