These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The Sharingan grove, Kitsune's Demonic Possession phases, everything Kenta does, the Warden's aka Orochimaru's illness, Tsukuyomi's vision of the future, some visions of alternate universes where things went worse, Alpha's utopia...
What an Idiot: Really Kushina, was it that great an idea to tell Kazama that Tsukiyomi is right about your actions in implanting the Kyuubi inside him when he's on the brink of a Heroic BSOD, having learned that most people he knew were manipulating him? You couldn't have waited until after to tell him you royally fucked up his life? As for what happens right after... well, sorry, but for the kind of stupidity you presented there, you kind of had it coming.
The Woobie: Loads of them, such as Jinchuuriki Sakura (from the Wave-verse), N (from the Cloud-verse), and Fem-Gaara (same as canon). For more emphasis:
Kazama: His whole life has been a lie and has been manipulated by almost everyone he thought was his friend, & his parents turned him into a weapon at birth because a senile amphibian told them to Because Destiny Says So (in a universe where destiny doesn't exist)! He has been corrupted by a God of Evil and is its Chosen One, Word of God has confirmed his status as a Cosmic Plaything, the Shinigami wants to kill him, and the closest thing he has to a father is the Big Bad, Tsukiyomi.
Chibaku: He probably has it the easiest, having spent a few years as a homeless bum... He's also dangerously pragmatic and ruthless
Kitsune has had it the worst. His life was made a living Hell by all of the village due to the side effect of Shisui's Genjutsu. His best friend Hinata died due to her father branding her with the Caged Bird Seal, leading to him making a deal with his three Kyuubi, turning him into a monstrous Serial Killer werefox. Then he formed an Odd Friendship bond with Kisame which is cut short by Kisame dying at Amaterasu's hands.
Kamui/Kakashi, moreso than either his canon counterpart or the other multiverse versions of him. After his father commited suicide, he was subsequently raised and mentored by Kenta. He got away from him and married Rin and had a baby, but then Kenta came back and kidnapped Rin and his baby, killing them and mailing the baby's corpse back to him after having tortured Rin to death. Kakashi killed him, but he was set back further much later than this when his genin team was killed. On top of that, he was forced to put down their reanimated corpses when Susanoo ruthlessly reincarnated them. Furthermore, in at least some versions of the multiverse, his dead best friend who he has based his way of life around is a possible Big Bad. Thankfully, the poor guy never had to find out the last part...
Zabuza's parents were killed right in front of him as a child because they had bloodlines, and he was later forced to kill his entire graduating class to save his village. He lost half his friends in a failed coup. Then he lost his best friend, Kisame, and apprentice Kimimaro - a pain he shares with Haku. In turn, she has the same horrible backstory from canon with the added bonus of being unable to save her mentor and father figure after he dies in the process of defeating Amaterasu.
Yugito: Was forced to fight and kill in a pointless war started by Orochimaru.
Naruko: She has deluded herself into thinking the multiverse works like a shonen manga, probably as a means of coping with all the crap thrown her way. Time will tell how long it lasts, too. It seems to have vanished after her fight with Kitsune's Kyuubi.