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Tear Jerker: Kekkaishi
Kekkaishi has a lot: episode 4 where Yoki turns evil because of the power but still pushes Yomi out of the way of a fireball and the way he whispered her name just before he dies was heartbreaking. Makes you cry happy tears when he's re-incarnated into his small form. The ending of Episode 7, where the Patissier ghost's little brother gives him a farewell so that he can move on disturbs your tear glands. And whoever DIDN'T cry at Episode 37 when Gen died does NOT have a soul, heart or TEAR GLANDS!!!!!
That one in 37 gets even worse when we find out he never received any of the letters his sister sent him, meaning he died thinking she hadn't forgiven him.
Even Masamori, who hadn't really shown any major emotions prior to that point, was visibly shaken (just not to the extent of his brother).
In chapter 343, Yoshimori's mom decides to seal off Karasumori, and that can only be done if she's sealed off along with it. And the reason she wants to do it is because she believes it was the only way she could show she cares for her family.
Her final good-bye to her husband is especially sad.
The true backstory of Karasumori, Tokimori, and Princess Tsukikage.
Also, the backstory of the Sousui and Suigetsu, Michiru and Kakeru.
Almost the entirety of episode 49, which concerns Aihi's life prior to joining the Kokuboro. Her death shortly after all the flashbacks is also really depressing on many levels.
Seeing Aihi's ex-lover (now an old man) and her fellow ayakashi/friend Shion retrieve some of the flowers she left behind after she died made it better AND worse at the same time.
There's Kouya's first death, when he's finally at peace after being killed by Madarao but is later revealed by Masamori. Before that, Kouya back when he was a normal wolf, sees his friend die in front of him.