ALL of the assistants in the Ace Attorney games. From Maya (her sister is murdered, she's the defendant in two cases, kidnapped and then the target of attempted murder, in which her mother dies in her place), to Ema (witnesses a murder, spends years believing she did it and watches her sister go from kind to cold), Pearl (pretty much all of case 3-5) and Trucy. It's just cruel.
The trope is actually invoked, by Moe the clown (of all people!) in regards to Regina, by bringing her to the trial of her father's killer, so that she can understand both the truth of her father's death and her own responsibility for Acro and Bat's injuries. This seems rather harsh but part of the reason is so Regina can understand her role in the case and just plain grow up.
In 2-4, Adrian Andrews applies too, especially since you're the one who has to break her.
Dual Destinies as a whole is not easy on Apollo. And then it gets even more savage on Athena.
Dangan Ronpa. The whole plot is about locking up 15 teenagers with special talents and different degrees of "cuteness" (from the nonexistant to the overflowing), pitting them against each other, telling them that the only way out is to commit murder, and seeing which one will break down first — and enough to start killing their companions without any mercy. The ones who get put through the grinder the most are Makoto Naegi (accused of the first murder, was framed for it and barely escaped, has to defend his companions and himself in trials, witnesses murders and executions), Kiyotaka Ishimaru (completely breaks down after his first real friend, Mondo Oowada, becomes the second killer and is executed) and Aoi Asahina ( takes her friends's deaths increasingly and incredibly hard, loses her own best friend as well, and with some push she snaps hard enough to try getting herself and everyone else executed). Let's not even get started on all the crazy shit that happens in the sequel...
Sakura from Fate/stay night, as revealed in the game's final route, Heaven's Feel. Poor kid spent years being carefully and brutally broken by the Matou family. Who got her raped, abused, and infected with horrible crest worms.
Hatoful Boyfriend: if you consider pigeons to be cute, (and why wouldn't you?) then the entire "Bad Boys Love" route is a big ol' break the cutie for pretty much every single character. Ryouta gets the worst of it.
Lux-Pain has, well, everyone in the main cast. Atsuki, Natsuki and Hibiki were broken in their backstories. During the game, this happens to two of the female leads: Mika, who was targeted by a serial killer (twice) causing Officer Mako Ando to be fatally wounded, and her best friend sent to the hospital, Yayoi who is driven mad by a mind parasite causing her to be jealous of her sister. She also tried to consult with a bunch of people she met online who were suicidal, but they ended up killing themselves. A few other Cuties, both male and female, end up snapping, like Akira, Sayuri, Yui, Honoka, and the list goes on. Forget curing Silent, that entire town needs one big hug.
It isn't actually the Nonary Game itself that does this to Clover, especially since she's already experienced it once. No, what breaks her is Snake's apparent death.
Akane seems greatly affected by their situation and the mistrust within the group, which combines with her Ill Girl attributes. While the behavior of present-day Akane is a lie, the events of her Nonary Game did traumatise her so much that she became a coldhearted manipulator.
Sky during the first chapter of Ascension. She loses her father, Tahn, and is too despondent to even speak to her Heterosexual Life-Partner, Aida. Even though Sky admittedly disagreed with her father a lot and fought incessantly with him, his death had emotionally devastated her.
18+Romance GameUnder the Moon offers love/hate story paths in which love interests become Bastard Boyfriends, so this trope is the order of the day. Each boy employs his own strategy to crush the Love Martyr heroine's spirit, but Softspoken Sadist Seizh is cutie-breaker extraordinaire. The more deranged he becomes, the more blatantly he treats the poor girl like a plaything.