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Tear Jerker: Shaman King
The flashback in the anime that shows how Mikihisa got his scars, not so much because of that but because of his wife Keiko. She'd just given birth to two baby boys and has been told that they both must die in order to protect the planet. That can't be easy for any mother to hear, poor thing.
Not to mention Yohmei's reluctance to kill one of the baby boys, which even brings him to tears. Made worse because a single moment of hesitation is enough for the Spirit of Fire to take a hold of Hao.
The ending of the episode "Winged Destroyers", when Lyserg decides to leave the gang and join the X-Laws. Worse, he still joins them willingly after seeing what they did to Boris, Millie and The Lily's Five.
Seeing what happened to the Lily's after they'd tried to help Millie protect Yoh and the others.
Poor Fudou, his past consisted of him being possessed many times by spirits (no doubt he misinterpreted their actions, since most spirits are not very hostile), which led to his hatred of them. Then after Fudou and his allies manage to find their way into Doby Village seeking to destroy Amidamaru since he escaped sealing before. Despite everything Yoh and his friends reach out to the boy and he eventually has a change of heart... only to run smack into Zeke/Hao a short while later. In the end Fudou and his allies are killed. Poor Fudou's spirit isn't even aloud to move on; Zeke/Hao just captures him and had his Spirit of Fire devour and absorb him. That just isn't fair man.
The flashbacks of Sharona and her girls as they fight Yoh's team, showing how each of the girls were rejected by their loved ones (Sharona, by the kid she babysat; Sally, by her workmates; Elly, by her boyfriend; Lilly, by her classmates (including a subtle yet very cruel flashback where she finds bullying message on her class's chalkboard), and specially Milly, who was deserted by her mother. From Plucky Comic Reliefs to massive Woobies in one, two, three...
In the anime, the deaths of the remaining X-Laws. Miina's was probably the most heart-wrenching of all.
Miina:(icicle spears rain down but Miina calmly turns to face Lyserg) "You are so kind Lyserg. We have always viewed compassion as a weakness, but perhaps through your kindness you will find a way to achieve what we X-Laws could not. Stop looking for people to follow Lyserg and learn to trust your own heart." (she's then skewered by the icicle spears)
After Zeke/Hao has removed and devoured Yoh's soul in the anime, the rest of the gang suffer a Heroic BSOD while remembering particular moments when Yoh was kind to them. Then all of them try to kill him in a blind rage.