Many fanfics out there have female characters being brutally raped, abused and tortured and that this is treated as being perfectly normal, loving behavior in a relationship. Most Fanfic Writers Are Girls. Think about it.
And there's a high percentage of slash fics that have guys being raped, broken and abused. This is seen as either hot or revenge for "not fearing rape in real life."
Stalking Is Love and even Loving Force are certainly present in professional fiction, but they are hardly endemic, especially more recently. Fanfiction features it to the point where it may not even be remarked upon.
According to various fandom-related comms, and confirmed by academic analysis (Camille Bacon-Smith's Enterprising Women being one of the first to spot the trend), a surprising percentage of fanfic authors who write rape do it because they've been raped themselves, and either it helps them get through the trauma, or they have a tendency to put personal experiences into their writing, or some other linking factor. So all decent rape fics, and at least some of the badly-done rape fics as well, carry a significant chance it happened to the author. Happy browsing...
In the DeviantArt fanfic "Good Landing", the astronauts aboard the Space Shuttle Columbia die on re-entry but continue as ghosts and don't realize they're dead until they land at Cape Canaveral. It's creepy enough to think about how they would have reacted to that, but at least they were only dead without knowing it for 16 minutes. One of the other astronauts (the sorta-protagonist) who's watching mentions how freaked out he was the first time he landed the shuttle. It turns out that he's the ghost of the Challenger commander. Since he died just after launch, he must have been a ghost when he landed the shuttle. So he and his crew members went into orbit and completed a perfect week-long mission before they came home and found out THEY were dead.
This Harry Potter fic has a girl frozen at ten by her grandmother. The fridge horror is named a few chapters in when it's mentioned she looks like her grandmother. Her possibly insane grandmother who was also dying. Who would bind her hands with magic if she had to scratch her shoulder. You gotta wonder why she chose to keep a child at the age she looks most like her....
In Eye Of The Fox: Kira outright confirms that if it wasn't for Rad/Naruto, he would have gone completely insane. And given that he leveled a whole forest once has to wonder just what Kira is really capable of doing if he lost the one anchor he still has in his life...
Pattycakes: Fluttershy, who has been derailed into an obsessed lunatic with a taste for mind raping other ponies into a temporary or permanent infantile state, is working on the drug she uses to do this, and comments that she needed to thank Zecora and Twilight for helping her create it - oh wait, she already has. Rainbow Dash, her first victim, wanders in and asks if this means she'll be seeing "a new brudder or sister". It takes a few seconds and then it clicks. Fluttershy in this story sees destroying other ponies' minds as an act of kindness, since they're so happy when they think they're foals. Dash has clearly seen this happen multiple times before, despite her mind being chemically wedged at a stage where object permanence is still kind of tenuous. The implications as to how Fluttershy "thanked" Twilight and Zecora are... unpleasant, to say the least.
In a Friendship is Magic fanfic called "Fluffershy", Rarity admits to having appeared in porn before she found her calling. Somepony's calling is represented by their Cutie Mark, which they usually get at around puberty age (and we know for a fact that Rarity got hers at around that time). Does this mean there's child pornography of Filly!Rarity?
The author later Jossed this. The fic was written before The Cutie Mark Chronicles had aired, and he had been working under the assumption that Rarity hadn't become a seamstress until sometime after she came of age. And at some point after that, he slightly changed Rarity's line from "Before I found my true calling" to "Before I opened up the boutique", greatly widening the timeframe in which her... "acting" could have occurred.
Hivefled is usually pretty blatant about the terriblethings in it. However, there's also this: Condesce, if her behaviour towards Gamzee (and the entire existence of Pyeran, the youngest of the kin) is anything to judge by, has some very creepy Shotacon tendencies. Now think about how young the Grand Highblood was when they first met. Later confirmed that there was at least serious creepiness going on when he was around puberty. He seems remarkably happy about it.
It's extremely common in the Homestuck fandom to write universes where SBURB/SGRUB never existed. This means that, in all those universes, the characters were not created by paradox-cloning of their ancestors but by natural reproduction. This also means that, in every universe where the game didn't happen but the troll characters exist normally, Sollux is the very likely the Child by Rape of the Psiioniic and the Condesce. Think about it — she's had him enslaved and immobile for thousands of years, she's demonstrated a romantic interest in him, and he had no known love interests with which to reproduce. And it's not like she'd be above that... In Hivefled, Sollux isn't, but he has a late half-sister who was. Also, Karkat's family line is the product of the Condesce and the Grand Highblood forcibly reproducing with the Sufferer as a way of torturing both him and Disciple (since she could never hand in a pail with him for fear of being caught), which has implications about Karkat's existence in other non-clone fics as well.
In Gensokyo 20XX, this is done In-Universe. Mokou did ask the question as to what would happen to Yukari once the warden gets tired of her and did say what would be likely.
On that note, what the hell happened to Yume? We never do find out what happened to her but we do know she died. Actually, we're never going to find out as she was cremated soon after death.
Was Reimu brainwashed and what is the effect of said mental scars?
The Writing On The Wall relies heavily on this, because the ending of the story reveals that Daring Do was not exploring an Ancient Tomb but a real life nuclear waste storage facility, thousands of years in the future. All of the things which had been set up earlier in the story - the sick workers, the metallic thorns, and the eponymous writing on the wall - become vastly more horrifying once The Reveal makes it clear what exactly the building was. Doubly so because the building may well exist someday.
The Reveal of the Soul Eater oneshot The Hand That Rocks The Cradle has some of this. Medusa kidnapped Stein and Marie's infant son to raise as her own Tykebomb, like she did to Crona in the manga. Except...She specifically says that she will make sure he is "everything his father had not been," refers to Stein as her former lover who disappointed her, and also says that she'll raise their son to be completely devoted to her. What else is she planning to do to this kid when he gets older?