Kano deals with her memories of a past life where she killed her own child, to the point that the personality is physically killing her.
Minagi: her Mother spends half the day either confusing her with her stillborn sister Michiru, or flat out not acknowledging her existence at all.
Misuzu, between being cursed for wanting to see her Mother in her past life and experiencing excruciating pain, for herself, the cast, and the audience, whenever she gets emotionally close to someone, and we won't even start with her Mother... Her pain is best summarized with one word... Gao~!
Yukito fills this role as well, from losing his Mother, the only person who he ever cared about, to being forced to complete her, and, by extension, his entire family line's, mission of helping the winged girl.
The heroine, Aida, from Ascension is the Stepford Smiler version of this trope. She was born a Half-Human Hybrid, exiled from her home kingdom, isolated from people, and was being hunted down by the Silver Order. When found by the Silver Order, her grandmother was murdered in front of her, and Aida herself was maimed and left for dead.
Yuka Otowa from Crescendo ~Eien Dato Omotte Ita Ano Koro~, since she was horribly broken in her Dark and Troubled Past. First, her parents were Driven to Suicide after getting in debt with the yakuza. Second, she was taken in by her uncle and aunt but her cousin started to sexually abuse her, with drove her to try killing herself. Third, her uncle and aunt did not believe her when she told them about the sexual abuse that their son was subjecting her to. Fourth, she was forced to live in a foster home where the other kids were scared of her due to her suicidal tendences. As a result she's the local Hooker with a Heart of Gold, pretending to be a Blithe Spirit when she's not...
Lily in Duel Savior Destiny adopts a cold, Tsundere attitude because she came from a world that was destroyed by Ruin. She's initially genuinely unhappy with Taiga because she thinks he's not taking his role seriously on top of his other personality flaws, but she warms up eventually. Or possibly heats up would be a better word considering she's still quite Tsundere.
Esperia in Eien no Aselia. She has great difficult in treating Yuuto consistently because of this. She's always nice, but she can be oddly standoffish and distant.
Tsugumi from Ever17 is infallibly cold and unpleasant to all the other characters and repeatedly brushes off questions about why a slight young girl is stronger, tougher, and faster than the rest of them put together. Alongside merry japes with nail polish remover and blowtorches, she also manages to fit in suicidal tendencies and, in one scenario, uses her superior strength to very nearly rape Takeshi. As a result, the point where she finally breaks down into tears and abandons all previous Jerkass tendencies is extremely satisfying, indeed. So much so that it happens twice, when the even more bitter and twisted Tsugumi from Kid's route is revealed to be the same character 17 years later, who has since lost everything she gained in the first scenario. She gets better, though, and at the end, returns to being the Tsundere that she had become after warming up to the main character.
Rider is Medusa, the Gorgon who earned Athena's envy and was cursed to become a monster exiled onto the Shapeless Isle, constantly fighting heroes intent on slaughtering her. She eventually degenerated into a monster herself, and was eventually put down by the hero Perseus.
Caster is Medea, who was cursed by Aphrodite to blindly love the hero Jason and betrayed her family to do so; eventually, she was rejected by Jason himself, and was forever branded a witch, a title that she sadly chose to embrace.
Rin Tezuka, in particular, sets the records. While her poker faced Cloud Cuckoo Lander antics are fun enough at first, you quickly realize that her inability to understand or be understood by others have left her alienated her entire life. She paints since she can barely put her thoughts into words, but when high expectations are suddenly placed on her art, she tries to change herself to match what's expected of her. She spends the next week alone in an atelier specifically outfitted for her use, painting nonstop: when Hisao decides to drop by despite how she has asked him to not do so... he finds Rin mostly naked, weak with exhaustion, and barely lucid from the attempt.
Hanako Ikezawa is a close second. Severely disfigured in the fire that took the life of her parents, she spent years in an orphanage and later alone in Yamaku High, with Lilly Satou as her only friend. If Hisao pursues her affections, he shall be careful: she'll sooner or later notice that he's trying to patronize her, and well-intentioned as he is, Hanako will only feel worse, and her Bad Ending has her bitterly and heartbreakingly tell him that she hates it.
Shiina "Misha" Mikado. A young girl who was bullied for being a lesbian and then came to Yamaku, she deeply fell in love with her best friend Shizune — only to be rejected. To not fully lose Shizune, Misha settled for staying by her side and stay friends: as a result, she became a massive Stepford Smiler, hiding her pain from her unrequited love constantly... and subtly talking about how she'd like to kill herself in Shizune's route.
A milder and non-romantic example is Lilly's sister Akira, a beautiful and tomboyish lawyer who actually hides the pain of being given a Promotion to Parent at age 19, when the Satous move to Inverness and their two girls (one of them being a blind 12-year-old) stay at Japan. Akira resents her and Lilly's parents quite a bit since she believes they did it because they couldn't handle Lilly's blindness, and she also feels guilty of not having done enough to raise Lilly as well as she could have done. (Though Lilly loves her and they get along well).
All the heroines are this to one degree or another. Emi lost her father in the same accident that resulted in her legs being amputated and still has major issues regarding letting other people get close to her to the point where her Genki Girl persona is a mask for her pain. In Shizune's case she has to deal with an Abusive Dad that forced her to spend much of her childhood taking speech lessons in an attempt to "fix" her as well as having major issues communicating and forming relationships with others due to her deafness, resulting in her being extremely lonely.
Mio, who uses her quietlysnarky, Emotionless Girl facade to hide the huge guilt complex she has about forgetting an old friend of hers, to the point where she doesn't feel any reason to stay in this world and is okay with swapping places with her permanently - at first, anyway.
Kurugaya - Cool Big Sis, Action Girl, and all around Ace extraordinaire. Except she's constantly bullied and treated as a freak and has no-one in the world she can truly rely on (at first, anyway) and created a whole other world just so she could finally feel something.
Haruka, one of the Genkiest of Genki Girls you'll ever meet covering up an incredibly depressed and insecure girl with one of the most fucked up families you'll see, even by Visual Novel standards. Or so it seems... at first, anyway.
Phoenix Wright: Ace Attorney gives us Lana Skye, the defendant of the bonus case of the first game. She is extremely cold to everyone because she locked away all her emotions, believing her little sister accidentally committed a murder which only she and Chief Damon Gant know of. Gant then blackmailed her to be his puppet to do whatever he says without question, she can't tell her (innocent) sister the truth, and thus locking away her emotions was the only way she felt she could keep her sanity.
There's a pair of twin sisters, one an obvious Genki Girl, the other an apparent Broken Bird Emotionless Girl. However, it turns out that Kohaku's genkiness is a mask for a completely shattered, emotionless psyche due to years of horrific sexual abuse at the hands of Shiki's stepfather/Akiha's father Makihisa Tohno, while the cold-looking Hisui is a Shrinking Violet who hides her feelings to keep Kohaku stable and honor how Kohaku took the brunt of Makihisa's abuse to keep Hisui as safe as possible.
Ciel was the previous incarnation of the vampire Roa, who has Born-Again Immortality. Once Roa manifested within her, she was forced to slaughter her town and commit unspeakable atrocities to the citizens. Although she was hunted down and killed by Arcueid (like all of Roa's other incarnations), Ciel survived due to her unnaturally high number of Magic Circuits. This piqued the Church's interest, so they took her and killed her repeatedly and in different gruesome ways to test the limits of her immortality. Eventually, once they found themselves unable to kill her, the Church decided to use her as an Executor. Ciel's entire motive for killing Roa for good is so that she can die for good.
Silviana, an anthropomorphic dog, from Wanko To Kurasou. In this game, anthropomorphic dogs are regarded and treated as regular dogs, even if people do know that they're much more intelligent and self-conscious. Her owner not only mistreated her and had her permanently locked up in a room, but also tried to play backyard breeder and make her breed before she even had her first heat. That resulted in her becoming an Emotionless Girl until she was rescued by the main character. She got better, fortunately.
Rena - the series' own embodiment of Adorkable cuteness - is heavily implied to have been one prior to the series, what with her mommy issues and heavily implied Rape as Backstory and Bungled Suicide. Her personal arc even has her cheery mask slip as she gives in more and more to despair.
Satoko, the series' punching bag also shows shades of this when her lingering problems with the rest of Hinamizawa are brought into the limelight. Mostly it stems from being ostracized by the rest of the village. Killing her own parents and having her brother disappear on her didn't help either.
Rika. Being Really 700 Years Old and being murdered every few weeks doesn't exactly make for a healthy mindset. It's very well hidden at first, but towards the end of the question arcs, she shows glimpses of this behavior. When she finally gets an arc centered around her, it becomes apparent that she's been broken every which way, and is frankly just waiting for it to happen all over again.
Shion. She is the second-born twin, and according to tradition shunned by her family (which itself is a step down from the normal tradition of drowning the second born - an uncomfortable fact she is well aware of) and eventually carted off to boarding school. When she returns, not only does she have to hide this fact from her family, but she has to hide her budding romance with Satoko's brother Satoshi, due to the stigma attached to their family. Eventually, she's found out, and the consequences are... nasty. Then Satoshi disappears; she suspects the family. In her arcs, these past traumas, set her on a murderous spree that ends with her own suicide (in the anime, it's an accident) when she realises what she's done. Oh, and she's not even the actual second-born. Her twin sister Mion (the real Shion) was mistaken for her on the day she received the Oni-tattoo, branding her as first-born.
Ange Ushiromiya. Many years ago, she was a cheerful little girl, but losing her family at a young age and a miserable relationship with her aunt and caretaker Eva made a stoic and lonely Deadpan Snarker obsessed with the truth of the Rokkenjima incident.
Bernkastel, known as "The Cruellest Witch" for good reason, then you find out that she is actually a personification of all the "Rikas" who were brutally murdered repeatedly and gave up on fighting destiny in Higurashi: When They Cry. She now wanders between the fragments doing whatever she can to ease the pain, revelling in the suffering of others.
Sayo "Yasu" Yasuda, the true identity of Beatrice, Shannon and Kanon, who is possibly the most broken character in the series. S/he is a Child by Rape, born as a result of Kinzo forcing himself on his own daughter Beatrice II; at just a few months of age, his/her mother dies by accident and his/her adoptive mother throws him/her off a cliff. Yasu survives the fall by a miracle (but with the implied mutilation of his/her sexual organs) and is passed off as an orphan at the Fukuin house so s/he can work for the Ushiromiya family as a servant. Suffering bullying from his/her fellow maids due to his/her clumsiness and young age, Yasu creates the Beatrice persona to cope with it and play pranks on them. S/he finds some happiness by falling in love with Battler, who makes a careless promise to "come to take Shannon away in a white horse", which Yasu takes way too seriously, becoming desperate when Battler leaves the family with little chance of returning due to some issues with his father's remarriage. S/he gives up on waiting for Battler after he forgets to send him/her a letter and creates the Kanon persona to keep "Shannon" company and cope with his/her body and gender issues. Then, Yasu decides to solve the epitaph and discovers the horrible truth of his/her origins and his/her broken body, making Yasu think of him/herself as a "furniture". For the following two years, this "furniture" complex and his/her conflicting feelings for George and Jessica make Yasu more and more unstable. The final nail in the coffin is when s/he hears Battler would return exactly the same year George was going to propose to Shannon. Yasu then decides to take everything down with him/her and plans the murders.