The deaths of Jiraiya and Kakashi, near-death of Hinata, destruction of Konoha, and having the truth of the ninja system quite brutally explained to Naruto almost breaks him. However, thanks to a few well-placed flashbacks, Jiraiya's book, and a pep talk from Iruka, Shikamaru and his father, Naruto recovers just in time.
Actually, if you think about everything that has happened in the series, Naruto kinda qualified as a 'break the cutie' from the outset. First, his father sealed a demon inside him as the only way to save their village, his parents are dead, and he grows up ostracized by the entire village. Then, finally, when things start looking up, his best friend decides to turn on him, cue battling with the power inside him for control, his best friend tries to kill their female teammate, tries to destroy his village, and everyone is trying to get him to kill said best friend. And his parents gave their lives to save him when he was a baby, and he was made to house the Kyuubi inside of him, the very same Kyuubi that his mother housed for a time, killed his parents, and tried to kill him. Really not fun.
Happened to Sasuke TWICE. Despite how he is now, in flashbacks he was shown to be a cute, naive kid. Until Itachi murdered their family... and then showed it to him... twice. The second time leading to his Face–Heel Turn.
To be more specific, the first mind rape and the actual massacre occur when he's about seven, and the second time, aged twelve-thirteen, had him forced to watch everyone being slaughtered hundreds of times, over and over, leaving him in a coma that only Tsunade is able to bring him out of. No wonder he freaks out, and then he gets worse and worse.
Gaara was six years old when he realized that no one loved him. His father hated him for his inability to control Shukaku, his uncle hated him because Gaara's mother, his sister, died in childbirth, everyone else hates him because he's a "monster"... he tries to hurt himself (in the flashback, he's trying to stab himself, and is disappointed when it doesn't work; later, he cries after being called a freak). His uncle tries to murder him — on his father's orders, which he actually questioned — and Gaara kills him in self-defense. He is effectively abandoned by everyone who should have cared. And the result? Sociopath at six, after he realigns his life's philosophy to fit with what he's learned; and serial killer by twelve, after he puts that philosophy into effect. No wonder he latched on to the idea of Shukaku as a "Mother" — the demon was the only thing making any effort to protect him (it was only doing so out of self-interest). When you've been starved for love all your life, anything will do. Even after he reforms (which Naruto brings about by giving him a good heart-to-heart talk about caring for others) and builds a family with his brother and sister, he is still haunted by his past — listen to what he says to Lee after saving him from Kimimaro, or what he says to Matsuri in what was one of the few good scenes in that filler arc. Six years of solid hate and horror? I'd call that broken. Made all the more meaningful by him actually getting much better in the current arc. Specially now that he can call out his old man on all the shit he did to him, leading the Kazekage to acknowledge said shit and telling him that Shukaku's sand was sorta directed by his mom's spirit, and that said uncle who attempted to kill him only did it on orders from his father. In reality, Yashamaru never hated Gaara — the person he actually hated was the Fourth Kazekage himself.
One other example is Nagato/Pain. He was a cute kid that Jiraiya trained and was so cute that he cried when he had to kill someone to save his friend's life. Then we found out about his childhood. He watched his parents get killed because they were trying to protect him from ninjas from Konoha (though it was mainly a case of mistaken identity), bonds with a dog and makes friends. He subsequently loses the dog when an explosive kunai blows it up as collateral damage from Konoha ninjas fighting some guy. Years later he loses his best friend because a Konoha ninja Danzo set him up to die. Not surprisingly, Nagato isn't too fond of Konoha.
Sakura now fits this trope. It went like this: Sasuke's defection, then Naruto failed to bring him back. Then Naruto went 4 tails against Orochimaru and Kabuto makes her realize it's at least partially because she made him promise to get Sasuke back and he agreed that he would, and he's still trying to do that no matter what. They find Sasuke but he leaves with Orochimaru and Kabuto. Danzo gives permission to have Sasuke whacked. Sai gets her to realize Naruto's feelings for her, and everything Naruto is going through: the burden of expectations she and the village pile on Naruto, and especially the suffering he's going through because of both her and Sasuke. Then Naruto calls her out on her painfully fakelove confession, outright rejects her, and then tells her that his promise to her was no longer the reason why he's trying to bring Sasuke back, for he has his own reasons for doing so. And then, she tries to kill Sasuke herself and fails, since she just can't go and kill the only guy she ever loved, no matter how far gone he is. And then Sasuke tries to kill her. If the girl doesn't end up as a Broken Bird, it'll be a miracle.
Also Kakashi, who was entered into the world of shinobi at the ripe old age of five and became a Chunin at six. Even with someone like Minato as his teacher, he must have seen some pretty bad stuff. And that was before his father committed suicide in front of him. Jeez, so much for a happy childhood!
Haku watches his Mother get killed by his Father and then kills his Father. Now an orphan he's forced to live on the streets fighting off wild dogs for food. Ends his life as Zabuza's weapon.
Itachi of all people. He witnessed the horrors of war at just four years old, then grew up to dedicate his life to peace. Unfortunately, the Uchihas decided to attempt a coup and his father made it clear he saw him as a weapon and not a son by forcing him to spy on the village. He then became a double agent and put his faith in the Third Hokage to solve the issue through negotiations, but due to Danzo's interference and the Uchiha's stubbornness, this fell through. His best friend tried to use mind control to stop the coup, but was overpowered by Danzo and shortly thereafter committed suicide in front of Itachi so he'd be strong enough to stop the coup. Stopping the coup, unfortunately, entailed killing his friends, family, and lover, tormenting his beloved little brother and abandoning the village to lead the life of a wanted, hated fugitive at the age of thirteen. He then spends his time spying on Akatsuki for Konoha while waiting for said beloved brother to kill him and avenge the clan. Did I mention that he was battling a terminal illness too? And he still managed to die with a smile on his face.
Obito also counts as one. The dude was basically an Uchiha version of Naruto: he grew up without ever knowing his parents, he had a one-sided crush on his female teammate Rin, who was in love with his rival Kakashi, and he dreamed of becoming Hokage and bringing peace to the world. His dream and entire right side is crushed by a boulder while saving Kakashi, and he makes Kakashi promise to protect Rin. He is rescued by Madara, who tells him that he can't ever be a ninja again and goes on to tell him how pointless the ninja world is and how it will only bring him misery. Obito refutes his ideals and goes through a painful rehabilitation process, with the only thing to keep him going being the thought of his friends. And when he finally leaves what is the first thing he sees? Rin dying by Kakashi's hands and the realization that Madara was right. No wonder the dude lost it.
