This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Shugo Chara!
Though not quite as sad as some of the other stuff listed, in Shugo Chara!, I was almost in tears when after Tadase confesses to Amu, and is later at her house. Ikuto walks out of her room and confesses that he'd been there the whole time, including during Tadase's confession. Tadase's reaction was heartbreaking for everyone involved, including the audiance. And then the aftermath, after Tadase left Amu tells Ikuto that she HATES him and leaves the room to go after Tadase. That was the last time we see Ikuto before Easter createsDeath Rebel. Then, there's also what happened to Tadase's dog, Betty.
Ikuto and Utau's back-story is pretty heartbreaking, especially regarding Ikuto. Their father abandons them to avoid being forced to give up the violin and run Easter and their mother is so devastated that she falls ill and is unable to care for them. They have to move in with the Hotori family, and Tadase's mother treats Ikuto very poorly due to being jealous of his mother (this was toned way down in the anime). Ikuto then has to go on the run and avoid being forced into working off his father's debt to Easter, and that means leaving behind his little sister and best friend. He's forced to turn the other cheek when Tadase confronts him about it so he doesn't get involved in all of Ikuto's problems and potentially get hurt. He goes looking for his father and cannot find him, and when he returns he is forced into Easter anyway with the threat that if he doesn't due their bidding, they will go after his mother and Utau. He spends many years alone and searching for the Embryo to free himself until one day he decides to take the Dumpty Key back. This involves going to Tadase's house, where he finds that Tadase's beloved dog Betty is dying so he plays her a melody on the violin to help her go peacefully. Tadase comes and sees this and misinterprets the scene and becomes angry, and Ikuto cannot explain because Tadase might get dragged into Easter with him. He then runs off with the Dumpty Key leaving Tadase to believe he's a thief and a curse that killed his dog and made his grandmother fall ill. Ikuto has spent half his life isolating the people he loves because he doesn't want them to get hurt. And that’s just leaving out all the crap he is put through during the Death Rebel arc. All in all, the Tsukiyomi siblings need a big hug and a blanket.
Kairi's confession to the Guardians almost had me in tears. Sure, we knew all along, but the creepy smile on his face, and the visible shock and hurt on eveyone's faces as he mocks the friendship they thought they had just feels like a stab in the chest. Especially when we saw his inner conflict and some of the genuinely sweet moments he had with Amu and the others. Even though they make up later.