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Tear Jerker: Shaman King
When it's revealed that Jun's guardian is Lee Pai Long, the famous Kung Fu movie star, then we learn the poor man was murdered specifically by the Tao family just to become Jun's puppet.
Watching Pai Long go berserk once he's freed from the Mind Control spell, thankfully, he gets over it.
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.
At least his spirit was likely freed along with all the others that had been devoured when Zeke/Hao was beaten.
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 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.
Horohoro's backstory in the manga, involving his former crush. dear God. It gets worse when Kororo reveals that she was Damuko the whole time!
During Yoh's group invasion of the plants, Faust is killed...only this time there's no one left to revive him...poor Ryu gets incredibly upset that his teammate and friend is dead, and even cheery Yoh seems to be affected. Of course it's abit bittersweet, since he can finally be together with Eliza completely now that both are dead.
The last few chapters in the manga, when virtually every character ever, living or dead returns on a train, Chocolove and Lyserg get to reunite with their dead parents, and everyone else with their loved ones. Hao even gets to meet Ohachiyo and his mother again!