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Tear Jerker: Gakuen Alice
The entire latest arc of the Gakuen Alice manga, from about chapter 90 on, made this troper bawl like a baby. First, Hotaru's older brother telling her that he really does love her, and he never forgot about her like she assumed he did. Then, the main characters go back in time to observe how Mikan's parents met. This culminates in her father's violent death, caused by a boy he essentially helped raise but orchestrated by the Big Bad. Then, flash forward nine months, to Mikan's birth, and a daydream/vision of her father's ghost holding the baby he never even knew was conceived. "Look, Yuka, it's a girl! She's so beautiful... Our Mikan..." SOB.
Far earlier on, there was a tearjerker that basically amounted to: "I am not crying over a penguin. I am no—- PENGUIIIIIIIIIIIIIIIIIIINNNNN!!"
The final arc, Mikan is going to lose ALL HER MEMORIES of Alice Academy (her friends, her guardians, her PARENTS) and even poor Bear is depressed by this. It gets even worse when Hotaru decides to save Natsume for Mikan and goes back in time to the point where he was injured in with Nodacchi and Subaru; the punishment for saving his life is that the Imai siblings disappear. Remember when this story was happy?
Most of the manga from about chapter 90 on (and other situations before that, possibly). Particularly Yukihira-sensei's death, and the aftermath