Ah, Tsukihime, what form of angst don't you have. One of the characters is the seemingly cheerful and carefree maid Kohaku. Spending her childhood locked in a room and being raped daily by her master, Shiki's adoptive father Makihisa Tohno, and doing so to protect her twin sister Hisui from being raped as well, made her a literal Emotionless Girl: she put on on a horrible cheery mask to hide her (lack of) feelings (while Hisui became a melancholic Shrinking Violet who feigned emotionlessness to not perturb her further), and in some routes of the game, she plots to kill every member of the Tohno Family as revenge.
Some? Just because you never see the effects in the other routes doesn't mean she wasn't doing it. As a VN, it makes the most sense to assume that everything's exactly the same in all the routes except for those things which are changed by the player's choices.
Things aren't exactly the same in all the routes, though. The Near Side and Far Side routes seem to be almost completely separate, as shown by the differences displayed by SHIKI. In the Near Side routes he is the vampire Roa reincarnated and does not seem to have a psychic link with Shiki, where in the Far Side routes he is evil/crazy because of the Tohno inversion impulse and has a mind link with Shiki. He looks completely different in the two scenarios.
Also, Fate/stay night has Sakura Matou, who has a very similar backstory to Kohaku. While Zouken subjects her "only" to Training from Hell and the Matou crest worms, her stepbrother Shinji rapes her repeteadly.
Her adoptive uncle Kariya Matou was a victim of the same sort of Training from Hell via the crest worms, partially because patriarch of the Matou family Zouken liked to watch him suffer.
Jigoro Hakamichi, Shizune and Hideaki's father, of Katawa Shoujo. He not only frequently insults his children, Shizune's friends and the student council, but also has refused to learn sign language to speak with his deaf daughter, and has tried for 12 years to get Shizune to learn how to speak, unwilling to accept that she is unable to do so.
While really more of an Abusive Uncle, Teppei Hojo from Higurashi: When They Cry definitely fits this trope. He beats Satoko and forces her to do chores for him, threatening to burn down her beloved brother's room if she doesn't comply. It's revealed later on that he's also a pimp, and is engaged in a fraud scheme with one of his working girls (Rina Mamiya) to scam half a million yen out of Rena's father. Teppei's fate changes in each of the three arcs he appears in, and none of them are pretty. He is murdered by Keiichi in Tatarigoroshi-hen; murdered by Rena in Tsumihoroboshi-hen; murdered by Rena, Keiichi, and Shion (all together) in Tsukiotoshi-hen; and arrested by Child Services in Minagoroshi-hen.
Though she is rarely mentioned, Satoko's aunt behaved in a similar manner. It didn't end well for her.
In Umineko: When They Cry, Rosa Ushiromiya has a very troubled relationship with her daughter Maria; when she isn't being extremely protective or overindulging her, she's slapping her across the face and yelling at her.
Rosa herself was on the receiving end of this trope along with her older siblings, and their father, Kinzo, makes his disdain of his own children quite clear several times in the series. And although he did genuinely love his illegitimate daughter Beatrice Ushiromiya, he deluded himself into thinking she was her mother and his beloved mistress reincarnated, leading to him raping her and getting her pregnant.
Grave from Symphonic Rain who physically abuses his daughter Lise just because her singing reminds him of his wife who left him for a singer