Tear Jerker / The Legend of Zelda: Phantom Hourglass

• When Link finds the Old Wayfarer's hideaway, there's a message left for his estranged son.
  Old Wayfarer: To my son, Romanos. If you're reading these words, you have found my true hideaway. Which means you also have developed a desire to find your own way in life. Know that I'm truly sorry for putting you and your mother through so much. I'm well aware that I'm the world's worst father, leaving you both behind. There's so much about the ways of the world I don't understand. Such as why the Ghost Ship appears and steals people. Where do its victims go? I have decided to dedicate my life to finding out the answers. If I fail to return, please take care of your mother. And please forgive me.
• The revelation that Linebeck accidentally saved Jolene from a sea monster and traveled with her before he made off with some of her loot. He was so close to developing a real friendship and perhaps more, but...old habits die hard.
  Ciela: Oh, Linebeck...you really are dense, aren't you?
• The final battle. It looks like Link and Tetra are about to get all of their life-force sucked out for good, but suddenly, Linebeck, of all people, starts to fight the monster off. This must be the hugest character development in a Zelda game EVER! (Not even Midna managed to change her ways that much). After all you've gone through alongside this Jerk with a Heart of Gold, he's finally proven that he's more than just a selfish idiot...and suddenly, Bellum comes up, possesses him and transforms him into a monster himself. Your only choice is to fight him, right after he got his Moment of Awesome. Made worse by the fact that he weakly calls out to Link, just before the transformation is done.
  • It's even more tear-inducing in the manga adaptation, where he almost commits suicide to stop Bellum, and it takes a time sphere to stop him. As he holds the sword to his neck, he tells Link that he really did like travelling with him, and tells Link to grow up to be a better adult than he ever was.
• When Link finds Tetra turned to stone, his expression is heartbreaking.
• Hell, in this game just dying results in the single most heart-wrenching six notes in the series.
  • The Game Over sequence itself. The way Link keels over with a weak gasp, his eyes glazed and staring into space and his mouth agape, the way the camera slowly zooms out from his lifeless body and the music, it makes it look like the ending to a bad-ending fable.
    • And there's also what happens if your boat takes too many hits while on the water. It's notable since this is one of the few times in the series where a character reacts to a Game Over, that being Linebeck shouting "W-We're going down!" as the ship starts to sink. What's worse is that this is also a Game Over that kills not only you, but somebody else as well.