In the Jackie Chan Adventures fanfic, Queen Of All Oni, when Jade's astral form is captured by Lung, Daolong Wong's apprentice, he uses extreme light to torture her into submission, even BURNING HER EYELIDS THROUGH!
And back on the GDI side: Zone Troopers and their railguns. They have ultra-durable Powered Armor, inhuman accuracy thanks to their sensors, can penetrate armor and buildings effortlessly, and the Nod infantry regulars facing them don't even have standardized rifles, let alone equipment to compete.
The "smart" claymores. They're small, innocuous disc-like devices that can be attached to walls or ceilings. If you're wearing a recognized uniform or IFF tag, it lets you pass. If you're not, it will hit you with a cloud of hypersonic shrapnel and white phosphorous that leaves the victim spread across a room as nothing but blackened meat and shredded equipment.
And by the same author, Forward, a Firefly fic that doesn't skimp on the horror from the series.
In the first story arc alone, you have River and Jayne being graphically tortured by Niska. Then later on, you get more graphic brutality with the Reavers assaulting an Alliance ship.
Inducer psychics. You think River was kind of creepy? She can only read your mind. In this story, one of the other projects the Academy was working on were Inducer psychics, who can alter and control your emotions and feelings. But its worse than mere Mind Manipulation; there is no defense against them, even if you know what they're doing, and their effects are lasting. If an Inducer makes you hate someone, you'll keep hating them for no fathomable reason. If the Inducer makes you love someone, you'll still love them, even if you hate them too, again for no reason. Many of the story's reviewers found the description of the Inducers to be terrifying, and this became even more pronounced when they learned the entire story arc introducing them involved one actively controlling the entire crew for her own ends. Including River.
Also in "Charity", it is shown how River gets a full blast of the emotions, thoughts, and history of someone as she kills them in close quarters, triggering her Out, Damned Spot! moments. This apparently includes Reavers.
Pain erupted along Jenkins' body as ten thousand tiny, thread-like razorblades ran across his skin, into his body, slicing apart muscle and bone and blood vessels. He tried to scream, but blood erupted from his mouth and nostrils and flooded into his lungs. His weapon fired wildly into the air for the few moments his arm remained attached to his body.
It ended a merciful moment later, when the buzzers found his brain and surgically sliced it apart, ending all consciousness. Jenkins' armor crumpled to the floor, weeping blood from a dozen rents and holes.
An Axis Powers Hetalia fanfiction called Awakening has Canada and America being taken as prisoners of war by the Germans. They are then sent to Auschwitz and experimented on by Dr. Mengele. Canada has blue dye injected into his eyes, while America is dissected alive and infected with tuberculosis and typhus.
The Weakest Link combines Adult Fear and Forced to Watch to ensure maximum Nightmare Fuel. Four of the youngest nations; Iceland, Latvia, Estonia, and Sealand; are kidnapped by a Complete Monster who sends America, Sweden, England, Lithuania, and Russia videos of the children being tortured. Scenes include Latvia's vivesection and Estonia being set on fire to make sure you can't sleep.
Old, old Fourth Doctor and Sarah Jane fanfic in which SJ awakens from a nightmare, in which she and the Doctor have suffocated in the TARDIS control room. At which point he comforts her, pecks her on the forehead, and carries her through the closed doors of the TARDIS, holding her so that she can't see the two dead bodies on the control room floor.
Bridgette's nightmare in Total Drama Comeback begins with a blood-stained Bridgette huddling in the corner of the shack, crying in pure fear after having just witnessed Geoff's murder. Suddenly, she hears snapping twigs and the creak of a door. She also sees Ezekiel's toque. Is it him here to comfort her and get her away from the camp grounds, just like Geoff tried to do? Nope. Its a cleaver-wielding Eva, back from a killing spree of everyone in camp. Long story short: Bridgette's next!
There's a writer on ff.net whose volume of work consists almost entirely of extremely gory, badly-written, but extremely disturbing short stories in multiple categories in which a character randomly dies gruesomely, most of them titled "(Name Of Character) Dies a Horrible Death". Interestingly, the extreme badness of the writing makes the stories even more nightmare-inducing, seeing as the language is abrupt and casual and stilted, as though a kid was writing them without putting any serious thought into it or feeling as though there was anything serious about the stories. Just take a minute to think about what kind of person would write like that....
The off-screen seizing of the Dursleys. This is also a Crowning Moment Of Awesome for everyone (read: the entire fandom) who wanted these characters to get their just deserts. The same goes for Fudge and Umbridge at the end.
The entire scene in the Great Hall. Voldemort orders Harry to open the Lament Configuration for him. If you've ever seen a Hellraiser film, you know what happens next.
Harry's own disturbing nature throughout the whole thing. After opening the Configuration as a boy and causing the death of the Dursleys, he ends up... well, different. His obsession with rebuilding the box, his Briar Patching to get Voldemort to call upon Pinhead and company, and especially the steps he's willing to take, including allowing Ron and Hermione to get hit by the Cruciatus Curse to reach the above, show how warped he's become.
There's a sequel which is even more disturbing, All Problems Solved, due to the constant undertone of dread that permeates it. Draco wakes up at St Mungo's with a hole in his memory and slowly begins to realize that something has happened to his wife Pansy Parkinson and most of his associates. As he tries to fill in the gaps in his memory, it's pure Paranoia Fuel with a bit of Adult Fear to spice things up. The worst part is what's become of Harry and the puzzle box: Harry runs a successful company that creates things based on the magical theory behind the box. As for the box itself, he keeps it at company headquarters, behind security that's laughable, despite the numerous attempts to steal it. He and his circle even had a bet going on how long it would be before Draco came for the box.
A Rose and a Thorn, a Sonic the Hedgehog ficseries on AdultFanFiction.net. Especially during the second fic, in which Shadow is tortured by GUN, has nightmares about it after being rescued, and then proceeds to stab an illusionary Amy in both palms with knives during a fit resulting from his experience at the GUN facility.
"Control", an Azumanga Daioh fanfic. It's extremely well-written, includes some well-crafted Fan Characters who manage to avoid Gary Stu territory, it takes some "controversial" approaches to some characters (especially Yukari) without straying too far out of line... and if you've ever considered trying hard drugs before reading this, you never will again. It's rated M not just for some Lemon scenes (some involving rape) but also some of the most graphic violence ever seen in an Azumanga fic (as well as explicit accounts of the horrible pain of drug withdrawal).
The entirety of "He had no fingers", a sort of Cosmic Horror StoryNaruto fic, starting with Naruto's body and spirit getting warped beyond recognition by the Nine-Tails until... well, the title is indicative. "Highlight" right at the beginning: Naruto's belly opening up and DEVOURING Kakashi (and Naruto then feeding the bits to passing strays). And that's the mildest thing in the whole fic.
The aptly named horror fic Nightmares. This is a fanfic of The Brave Little Toaster, a movie already known for Nightmare Fuel. The story is a series of first-person vignettes, detailing the horrific dreams of the other four main characters during Toaster's Nightmare Sequence. It starts out only slightly unsettling, but gradually builds up, accumulating in the truly horrifying Chapter 4.
This Tales of Symphonia fic Blood Is Thicker, one of the few vampire fics that really stands out, with dread starting only a few paragraphs in. The Big Bad is Lloyd's grandmother, Maetala, a caliber that makes Alucard look tame. After turning Lloyd into a vampire, she twists and manipulates him into giving up what little humanity he has still retained encouraging him to eat a boar alive is probably the least horrifying thing she does all fic long, and the results leave Lloyd, a canonical Determinator a psychological wreck and makes it horrifically believable.
You wouldn't think horror and Lucky Star could go together...until you read Ahoge. Tsukasa is (arguably) taken down to extreme ditz levels when she thinks Konata's Idiot Hair could grow into a plant... This is either badass or just plain Character Derailment. The last chapter is an especially horrifying as Sojiro Izumi takes revenge on the entire Hiiragi family through Cold-Blooded Torture. A, umm, nail gun is involved at one point. You probably won't look at Tsukasa the same way again.
There are a lot of disturbing Pokémon fics out there, but the second half of Reunion is just downright disturbing and at times grotesque. It starts off as a slightly darker AAML fic, with a lot of funny scenes, and then—Butch gets his throat torn out by a Mightyena, a sadistic psychic Rocket elite who assimilates the minds of the humans and Pokemon he kills is torn apart as the souls he absorbed struggle to free themselves by growing off of his flesh, before throwing themselves to their deaths...with smiles on their lips... And it gets worse from there...
Much of the Evangelion fic And If That Dont Work qualifies, but really the standout if when the acid-dripping spider angel managed to turn the entry plug of Unit 02 into a vat of acid and the resultant fate of the pilot. This is even worse considering her fate is blatant Author Appeal; none of the characters view it to be a bad thing for more than a few sentences and Asuka herself considers it an improvement.
Shinji And Warhammer 40 K mostly manages to cancel any horror with mind-boggling levels of awesome, but plenty of things slip through. Sahaquiel killing who knows how many millions of people around the planet in less than a day by flinging parts of itself into various cities and utterly annihilating two of them wasn't exactly pleasant. The Zombie Apocalypse unleashed on Tokyo-3 was far worse, with zombies that teleport anywhere they want, can even infect the dead and heal quickly from almost any damage, only a bolter round to the head a guaranteed kill. The crowning jewel however is what happens when the Earth's Cradle crashes into Germany. Essentially, it combines the Necrons (kill everything), Tyranids (eat everything) and Chaos (corrupt everything) into an impossibly horrible amalgam that renders most of the continent barren and swarming with monsters, leaving nothing behind. The intimate accounts of some of the survivors are custom-made nightmare material.
Darker and EdgierRedwall fanfic Vengeance Quest is brilliant, but terrifying. The violence was one thing, but Guardcaptain Kiern's attitude is also creepy: he's pretty sure the actions of his sadistic co-workers are morally wrong, and lets them happen anyway. There's a scene where Captain Veneno rapes a prisoner in order to force her husband to spill the info they need, in front of Kiern, who's getting progressively more uncomfortable, but still doesn't do anything to stop him because there's no other way they'll get the information. Later on he talks to Big Bad Nightdeath Longclaws about it, essentially asking to be persuaded that it was okay to do this. Brrrr.
The description of Azkaban in Methods Of Rationality—especially the woman who accidentally killed someone, immediately went insane with remorse, and then is forced to relive the moment of the murder over and over by the Dementors. Also, the scenes where Harry is walking around protected by the True Patronus, giving momentary relief to the prisoners in the cells he passes, but forced to keep walking and leave them again to the Dementors, and hearing their screams to stay. The in-story Aesop is that Azkaban is simply evil, and afterwards Harry concludes that because the nominally democratic magical government allows Azkaban to exist and in fact runs it, he is under no obligation to obey the wishes of the majority.
An Invader Zim fanfic called Dark Harvestby Swing-21. Even the name screams Nightmare Fuel. A fanfic rated M for a very, very good reason. Starts out creepy, ends up with a horrifying Twist Ending... of Dib actually kidnapping Sara, and the poor reader learns that HE is the one that is stealing organs to keep Zim alive, who had apparently lost his own. Zim isn't stealing organs this time... ALSO, the mental image of Keef, loyal to Zim and...ahem..."donating" his organs, covered in blood and stitches gives the chills. Darker and Edgier, anyone?
Personality Conflicts runs on this and angst. First, you have Tommy's multiple personalities anthropomorphized as an Eldritch Abomination. Then, you have... anything dealing with Nyghtmayr or the Shadow Empire. Did we mention that since the main rangers are trying to get witnesses for Zordon's trial, children fight Shadowborg?
The Avatar: The Last Airbender fanfic The Chong Sheng Trilogy. First installment, War, ends with Ba Sing Se being carpet bombed to rubble while the characters are trapped underground listening to it and freaking out. The second installment, Peace, involves among other things Katara witnessing Jet's torture and murder at the hands of the Rhinos, and subsequently going on a Roaring Rampage of Revenge ... using their own blood to rip them apart, a side-story involving some original characters where a troubled soldier tortures his own father by slowly removing his skin in small patches and giving him an occasional hit of opium just to keep him conscious through it, and lastly, Zuko confronting and killing Ozai, who has lost his mind entirely to the point that he thinks he's fighting Iroh instead. Also, one of the aforementioned original characters is a borderline pedophile, and very heavily implied to be sexing it up with Azula.
The Avatar: The Last Airbender fanfic "When All Your Dreams Come True." The premise: Zuko succeeds in capturing Aang and his friends sometimes during Book One and takes them back to the Fire Nation. The reality: Sokka immediately gets tortured and killed, since the Fire Nation has no use for him. Katara gets her tongue cut out and turned into a gladiator-style "training exercise" for Fire Nation soldiers, to get them to practice fighting a waterbender. She eventually loses an eye, becomes known as the Widowmaker, and evolves into a sort of proto-Hama. Aang gets both his eyes put out and thrown into prison to live out the remainder of his life in misery. He goes insane. Toph wasn't even in book one, but also gets killed off for no good reason but to add angst. Finally, Zuko goes completely mad from guilt and drinks himself into oblivion, conjuring up detailed delusions of himself joining the Avatar and teaching him firebending, falling in love with Katara, bringing down his father, and ending the war. After reading, you feel like you want to scrub your brain clean of the images.
Some of the worse endings include Appa being killed and eaten by the swampbenders (and then when Aang is freaking out, they offer some of the meat to him), Suki being killed on the day of the comet leading to Sokka being incinerated by Fire Nation soldiers and Toph falling to her death, Azula's lightning hitting Katara at the Last Agni Kai and Zuko inadvertently gutting her with his swords, young!Azula and young!Zuko being caught listening in on Ozai and Azulon and Ozai murdering Zuko with lightning right there, Katara accidentally ripping Aang, Sokka, and Toph apart with bloodbending.]]
Counts of Blood is a good Buffy the Vampire Slayer that crosses over with the Muppets, but its portrayal of Count von Count is terrifying. For starters, he apparently cut up a mathemetician into over a hundred pieces and put them in small boxes, and early on in the story, removes the feet of the poor sap who took the pills he needs to curb his violent tendencies!
Anything Ann-Kathrin Kniggendorf (otherwise known as AKK) wrote for Adventures of the Galaxy Rangers. "The Lie" has a brutal rape depiction that can shock even the most veteran reader, and acts as a crushing inversion of Double Standard: Rape, Female on Male. It says something when the poor hero views having his soul ripped out afterwards as a relief! Her pre-series Supertrooper works are all the more chilling when you hear the violence and death described with clinical precision. Walking Through Nightmares depicts severe asthma, lung damage, and the inability to breathe in graphic detail. And then there's Raumjaeger. Oh, shit. The classic idea of "what if Nazi Germany won" played for all the horror you can imagine and then some. You will not be sleeping well after it, especially after little details like the human-skin lampshade. Worse is that Ann-Kathrin, like half of the fandom's writers, is German and English isn't her first language. The show itself? A kids cartoon from The Eighties.
Parts Of A (Bung)Hole. It starts off as a bit weird and angsty, with a Crack Pairing, though the author does his best to make it believable. The ending, however, is positively hellish. After learning that Beavis And Butthead (mostly Butthead) raped Daria & drove her to alcoholism & death in a drunk driving accident, Jane tears open Beavis' throat with her teeth while they're having rough sex & then uses his insides to paint a portrait of Daria on his bedroom wall. Daria fans do love them some Dark Fic, but ye gods...
The Never Never Land A Harry Potter fanfic where McGonagall takes in the grand-daughter of an old friend. It turns out the grandmother had possibly gone mad and created a series of potions to freeze the girl at ten. It's implied that the girl has also been kept locked up in the house for years with only granny and a house elf for company and was probably abused emotionally as well. Also, the kid is one Creepy Child. She talks like a robot and needs precise directions. When the grandmother kicked it she spent about four days in the house with the dead body, going about her business. The author promises Body Horror in later chapters.
One Mistake Too Many, a Wicked fanfic that explores what might happen if Boq's transformation hadn't gone as smooth as it had in the musical- ie, if Nessarose had decided that she should be the one to cast the spell. Here's a hint: the first chapter is called "Transformation Trauma."
Our little Doll, a Coraline fanfic, where the Other Mother rapes Coraline. The actual rape is implied, with just the preparation shown (Coraline being bound and having her clothes ripped off her body by Other Mother). Then we cut to the aftermath, with Coraline waking up in real world with no recollection of what has happened - until she gets abdominal pains so strong that she collapses. In hospital, the doctor says that she was violated by freaking knitting needles, prompting disbelief from her mother. And then it is revealed that Other Mother can take control of Coraline, forcing her to come to the Other World again and again...
Cupcakes, A My Little Pony: Friendship Is Magic fan fiction... where Pinkie Pie slowly tortures Rainbow Dash, then dissects her while she's still alive. The reason? To use her organs as ingredients in her "special" cupcakes. And the worst part? Pinkie thinks of the whole thing as a 'party', and is thoroughly enjoying every moment of killing her best friend.
Dalton contains the thoroughly crazy stalker Adam Clavell. He's got a wall covered in photos of his lust object, Julian, he stuck them to the wall with his own blood, and he's made a hit list consisting of a bunch of photos with the faces mutilated and the words off with his/her head written on the back.
The final part of chapter 26 begins with this author's note:
TRIGGER WARNING for blood, violent acts and images, and the behavior that revolves around this theme. If you are not comfortable with these types of scenes and images, I strongly urge you NOT TO CONTINUE.
The nightmarish dream world that Sleepwalker's Arch-Enemy Cobweb creates by possessing the mind of scared young Reality Warper Kevin Mac Taggart. The dream world is a shifting twilight world of ugly colors, half-seen images and distorted surroundings that threatens to grow and expand like a cancerous tumor until it consumes the whole Earth, engulfing the minds of everyone on the planet in its wake;
Cobweb himself, a demon from the Mindscape who thrives on the Cycle Of Hate caused by racism, violence and war, and actively tries to fan the flames of hatred that arise from such conflicts. He also brutally kidnaps and tortures Sleepwalker's Big Brother Mentor, turning him into a hideous monstrosity called a Dreamkiller, that becomes tied up in the brutal Mind Rape of one of Rick Sheridan's human friends, who's eventually Driven to Suicide;
John Edward Cicala, alias Jack the Ripper, the illegitimate son of a British nobleman and a nameless street prostitute who made a Deal with the Devil to turn himself into a demonic force capable of possessing evil men and using them as his People Puppets to go on a killing spree murdering street prostitutes;
Sleepwalker's Evil Counterpart Psyko, a human gang leader twisted by Cobweb's demonic power into a humanoid abomination that combines Hannibal Lecter's disturbing intimacy with his victims with the ability to make his victims suffer their worst nightmares and a healthy dose of Foe Yay and rape imagery that perverts true love and intimacy;
Sleepwalker's own psychotic breaks after he suffers a vicious Curb-Stomp Battle and Mind Rape at the hands of Psyko, which drives him insane and nearly leads him to murder his Heroic Host Rick Sheridan.
The disturbing rants of the Brothers Grimm, who's apparently a Psychopathic ManchildReality Warper who uses all sorts of disturbing fairy tale and toy paraphernalia in his crimes and who is prone to arguing with himself in an increasingly disturbing fashion, and whose idea of "performing" consists of kidnapping people and forcing them to watch disturbing sequences involving demonic toy soldiers ripping apart superhero dolls, witches juggling severed teddy bear heads, and skeletons juggling their own bones in choreographed dance routines;
In the first Halloween Special, we see Jack sitting in his cell on Halloween night. He's dreaming of the fond memories he had of hacking into pumpkins, ripping their guts out and carving their faces to resemble jack o'lanterns...and he's fantasizing about what it would be like to do the same thing to a human head.
Moonstone, a Manipulative Bitch who kidnapped several people as part of a twisted scientific experiment to analyze the physiological reactions of their families in stress situations;
Starting from a noble pirate on his Honeymoon, diving down deep into depression, to the point of starting a war to aleviate boredom, and then after a brief Hope Spot, Hook goes completely mad and starts trying to kill his wife. And then there's the fact that Tinkerbell is Peter Pan's mother, and in order to survive childbirth they had to use the magic flower from Tangled.
And Shego's fate. At the age of five years old, she's put into a spandex costume to fight in a war. And then she has to watch the Headless Horseman, who is already pretty frightening, kill her older sister. But then when she tries to burn the Horseman, and he puts on her sister's head to mock her. Watching her sister's head burn up puts her into a Heroic BSOD.
All of the inhabitants of Underland. Just the concept that if you're born to the wrong parents you have the chance of becoming a Devil, and it's implied this could be the fate of Peter Pan would be scary enough, but they're pretty scary. The Headless Horseman, who has the strength to drag a battleship under the sea, and absolutely cannot be stopped. And Alice, who's been taking smiling lessons from the Chesire Cat and it's heavily implied that she raped the magic mirror. Most rape is bad, but a cute little girl with a Slasher Smile demonically violating a piece of glass? Nightmare.
This VOCALOID fanfic, in chapter 6, involves Rin waking up in the middle of the night, walking down the hall, seeing eyes at the end of the hallway, and being "attacked" by it. If you read it carefully, it could be implied that whatever the thing was was attempting to rape her. However, it's revealed at the end of the chapter that the monster was actually "Caiden" and he wasn't trying to scare her.
Used, a House fanfic. The things Tritter does to House are pretty certain to give one nightmares, including raping him with his own cane, and a knife.
Seven Little Killers, an Axis Powers Hetalia fic in which... well, everybody dies. It starts when Switzerland is murdered, and Italy walks in on his dead body. Everybody blames one another, and at first it's all just he-said she-said and pointing fingers, but then the bloodbath starts. The fic is based around the idea that there are seven killers on the loose, each named after the color of the mask they wear, lead by the infamous, shadowy Black and trying to kill off enough nations to completely reform the world order. Japan, Italy, and Germany are the ones on the hunt for the truth. Some of the nightmarish highlights are America masquerading as Canada masquerading as America killing several characters and crushing Japan's fingers as payment for letting his other captives- including Canada-as-America-as-Canada- free, China murdering New Russia on the orders of the killer Yellow and then going bonkers over it, several cities being completely decimated to weaken their nations, America manipulating Canada into killing a boatload of people, including Alaska and Hawai'i- whose death scenes are both cut right away from, although Hawai'i's is over Facebook, for crying out loud- and... well... the entire thing really.
Orcs goes into fight with Tyranids resulting in two species merging into unstoppable New Devouer, that eats half of the galaxy
God Emperor Of Mankind dies only to be reborn in Warp as Star Father - Chaos God of Order
Then there is The Ophilim Kiasoz that destroys entire star systems just by passing through them
The Nex (Keyboard attempts to bite editors fingers off and snags a thumb, new editor takes over) the merest mention of which causes the scroll the stroy is written on to turn into a swarm of spiders that nearly devour the author of the story before a sentry gun destroys them.
Crimson Echoes has the scene towards the end when the team is exploring The Darkness Beyond Time... which is a horrifying enough concept as it is. But then you see the journal... "There is nothing outside the windows. I mean that. Nothing." And you realize the people who are there aren't all just frozen and they're... alive and they're aware and there are billions of them, and you realize all the times when you played Chrono Trigger, you put them there...
The Regular Show fan story Regular Addictions involves Benson going on a drug-and-alcohol binge because he is unhappy with his current life and wants to end it all. Since he's a gumball machine (lacking organs and what not), he realizes it leads to nowhere. What's one of the first things he does in his bout of insanity? He decides to kill Veronica, his ex-girlfriend who is said to have dumped him callously, while saying the lyrics of a song he wrote for her with a dark tone. As if that weren't bad enough, Mordecai had to keep it secret after Benson told him about what happened lest any other event could worsen the situation.
The CSI: Crime Scene Investigation fic Face The Music by Elm22 has a lot of this in the form of Grissom's kidnap and torture (and later Sara's as well). The fact that it's an extremely well written, well researched fic makes it all the more haunting.
Mercurial Cognizance, a deeply disturbing Durarara!! fanfiction that shows us what potentially goes on in Mikado Ryugamine's head. An evil doppelganger attacks Mikado, stabs him with a pen, and rapes him. All the while Evil!Mikado tells Good!Mikado that everyone has a dark side that needs to come out, while poor Good!Mikado is less concerned with the fact that he's being raped by himself than he is truly terrified of the fact that he himself is capable of doing something like that to another person. Fortunately it turns out to be a dream...and then Mikado looks down to see that his hand is now bandaged. And then he shudders and bursts into tears upon remembering the last thing the doppelganger said to him...
Doppelganger:It's not a dream.
The comic version of the Axis Powers Hetalia AU fic The First Cut: Or, The Angels of the Rye takes the implied horror of what the protagonist witnessed and shows it to the reader/viewer, showing aptly just why the titular first cut was hidden away. Namely the haunting images of Poland and Lithuania, who were last reported killed during the Terror several decades before the story, staring right at you, pleading for help. Also, the protagonist is their grandson.
From Dragon Ball Multiverse we have Universe 16 Pan being strangled to death by Bojack. When it looks like she is about to break out of it...he SNAPS HER NECK.
ThisAxis Powers Hetalia fic tells about five times in history that France died. Four of them (the Black Plague, the Battle of Hastings, the American Revolution, and the German invasion of France in World War II) were frightening enough, but the worst was the French Revolution, which tells how France was beheaded in front of his own people, was still conscious some time after, and finally awoke to represent France as a republic.
Some of the descriptions in Cori Falls's Pokémon fics. Some notable examples are "The Power That's Inside" where Meowth's narrative describes Pikachu's electric attack hitting Jessie and James as "frying flesh and bone alike", the brutal mass beating of Ash in "New Directions 1" wherein his many injuries are described in great detail and it's clear that if not for the healing lake he might have died, and Jessie's grandparents' beating of Ash and Misty in "Never Too Late". There's something unsettling about the image of two sweet old people pulverizing twelve year olds.
Experimenting Fearnote The site only allows users who are logged in to view the story due to its mature content, a Pokémon fanfic that details a 10-year-old Nando being kidnapped by a scientist who forces people to deal with their worst fears. Said kidnapping is the least frightening thing that happens in this story: Nando is stripped down to his underwear, chained to a toilet and tortured with high pitched sound frequencies, then is made deaf by the scientist firing a gun right next to his head.
By the time he sees said gun, he's been through so much torture that he ends up wishing it would be used to kill him. Let us repeat, a ten-year-old boy had been put through so much torture that he wanted to die!
Melimsah's fanfic Never Alone is Teen Titans fanfic that take place after the episode Haunted, and it continues from there in its own alternative way. The story is about Robin who afterwards thinks that Slade is out of his head now that the mind-dust is out of his system, only to once again see Slade when no one else can. As Robin try to find out why, it gets more and more hinted that it isn't the mind-dust again that is behind Slade, but simply his mind losing itself to the grip of paranoid schizophrenia. Slade himself goes from playful teasing and insulting to Mind Rape and downright physical assaults, causing Robin to somehow hit himself into near death. As the story goes on, Robin's condition worsen each day while Slade becomes more powerful, and he sends Robin into a spiral of delusions and self-destructive behavior, and Breaking Speech him so badly that Robin goes from a strong leader-type of hero into a scared, self-loathing child, and when the other Titans finds out, they've no idea how to treat him or how to force Slade out of him.
Minty's fanfic on Encyclopedia Dramatica.se that is a supposed Toy Story fanfic in which the main heroine is tricked into going into a home group and her toys are taken away by a woman by the name of Nicole. The story itself makes Lotso from Toy Story 3 look like a kid's show host.
Though the premise of quarians uplifting the Nazis in Uplifted is a scary concept in itself. The fact that Hanala'Jarva unwittingly tricks Joachim Hoch into exploring a Prothean Dreadnought, only to find out that it was in actuality a dying Reaper packed with Roman Legion Husks and Collectors.
Chapter Nine of Uplifted: Last Days... Oh God...
Imagine, if you will, that you live in the Milborough of The New Retcons; not only do you live with the knowledge that you got the sweetheart deal you did on your mortgage because you live on what used to be a nuclear test site, you have to contend with crazy old Elly Patterson who's convinced that it's the early eighties. Factor in the fact that she had a volatile temper back when she was nominally sane and you realize that her lazy, image-obsessed jerk husband's refusal to do anything about her (as well as the law's inability to lock people up without due cause) has left you having to deal with a human bomb.
Robo Bando is so filled with graphic violence and torture scenes that makes Elfen Lied family friendly.
And the most chilling thing is that the stories are presented in a way that's a Deconstruction of the Decepticon/Human pairing by showing how a 'Con might really act if they ever got attracted to a human; up to and including attempted murder, the complete fear on the human's part and the complete one-sidedness on the 'Cons part.
There used to be a Total Drama World Tour fanfic (now removed) called "Pineapple Rape". It involved Alejandro shoving a pineapple up Heather's vagina.
Well, think about this. There's a war going on. Has been for the last million years. But, y'know, you're pretty well off. You live in a lovely, peaceful Neutral settlement with a Reasonable Authority Figure, though he is a bit of a The Cynic. Sure, there's the occasional JerkassMiles Gloriosus you have to deal with, but, I mean, who doesn't? Life is going great, really... until one day, a big, bad Decepticon comes. Not good, y'see. I mean, "violent creatures, ruled by whim and cruelty... macabre corpse-gray monster... glowing red visor... " y'get the picture. Heh, gotta love the flattery, though. And oh, did I mention he just brutally offlined that aforementioned Miles Gloriosus with his bare servos within one paragraph of his intro? Quite awesomely, may I add. Always take pride in your work. Good philosophy, that... Sorry, getting off track. So hey, like the title says. Massacre.
 has very little, even with its SIU AU version, but chapter 6 changes everything. When we're first introduced to the alchemist Ronald, he's a Large Ham, typical Power Rangers brute before it's revealed that all the defeats he's suffered over time has turned him psychotic and out for revenge against the Rangers and he takes it out on themby torturing them with the worst pain imaginable. And then his death makes it WORSE.
The Big Time Rush fanfic Big Time Obsession (Rated M for a reason). It involves they boys and their friends trying to protect Camille from a serial killer/rapist named Hyde. Eventually though Logan is abducted and tortured by said rapist. Don't worry, he's saved, but people still get killed in the process. For details, of the shit Hyde does in the story he tortures a naked Logan over a two way camera, unless Camille stripped for him, forces another hostage to have sex with Logan, he kills Frieght Train, and a good samaritan that tried to help Logan. Now heres the character Hyde himself, turns out he's actually a split personality of one of the detectives on the case. We meet another personality of his - a child who Hyde shifts to when Logan shoots at him.
Imagine you're imprisoned in a underground facility where no one will ever find you. Everyday, a scientist performs experiments on you such as exposure to extreme heat and cold, enduring sounds that will paralyze you, and cutting off your hand. No matter what you claim, said scientist insists that not only are you not human, you're not sentient and are incapable of feeling pain. Now imagine, this is all being done by your mother. Welcome to the Danny Phantom fic Phantom of Truth.
The Simpsons fanfic Death of a Simpson is played out like another Sideshow Bob episode, only the differences are that Bob has finally lost his mind completely, so that he actually see people and things that only he can see, that he finally has killed Krusty in the most gruesome ways possible, that he's targeting Lisa instead of Bart, planning to simply torture her to death, and when that fails, it seems that his spirit tries to possess Maggie to be the new him. A chilling tale of one madman's revenge against the young people he feels ruined his life to that of a hunted, crazed animal.
Through the Monitor, a  Fanfic that has characters from our world become characters in the Sonic universe, has as a main villain Void from Sonic Shuffle, who in this universe is reinterpreted as a Psychopathic Manchild. As a result, every scene he's in is Nightmare Fuel, but the scariest and most evil thing he does is in chapter 56, when he sinks a cruise ship killing (almost) everyone on board Forthe Evulz. Sure, they were saved, but it's still scary and a Moral Event Horizon.
In chapter 13, the murder of the Thorndykes save for Chris because they had the Green Chaos Emerald. It serves as Eggman's Moral Event Horizon and one of the fanfic's darkest moments.
The Fragility of Time has Rubeus's murder of Mimete in chapter 34, followed up by his murder of Eudial one chapter later.
Making it worse is how he does it: exploding her Fire Buster and then impaling her with his spheres (which he also did to Mimete) Fortunately, he pays for it.
Even worse is her reaction when she loses Eiron's Star Seed. Said reaction boils down to Kill 'em All.
Missing has Sebastian kidnap Kurt and hold him captive for a year, heavily drugging him, conditioning Kurt to be his baby, and threatening to kill him if he resists his "daddy." The forced infantilism is bad enough, but the scariest parts of it are Bud and Kari (Sebastian's friend and the girl he kidnapped and conditioned the same way) and their relationship, and both of the sex scenes.
An Outsiders fanfiction, The Days That Changed Everything, has Sodapop and Ponyboy being taken away from Darry and ending up abused for six and a half months in separate foster homes. James, the father in Soda's foster home abuses his baby daughter Emma, and locks Soda in his bedroom when he tries to protect her and tells him he is wrong for trying to stop him. To keep her safe, Soda makes a deal with him that if he doesn't fight back against James, he'll leave her alone - leading to James burning the word "WRONG" into Soda's shoulder with a cigarette, threatening to hurt Emma if he struggles. The worst part? When Soda goes back home, James ends up killing Emma. But as horrible as that is, it pales in comparison to what happened to Ponyboy: When Ponyboy did something that Robert, the father at his foster home, didn't like, he would drag him out to the backyard, force him to dig a hole and lie down in it, and then bury him alive with only a straw to breathe through, nearly killing him. Worse, he does this twice, once during a thunderstorm. Their experiences leave both boys badly traumatized.
Episode 66 has a very disturbing example, a la Event Horizon. Astorath is called away from his fight with Sonic and friends by a distress signal from his flagship. When he arrives, he finds the bridge deserted and his escorting fleet gone. He soon discovers a security tape of his crew graphically tearing each other apart and mutilating themselves as Dark Tails speaks to them.
On that same note, the fate of the people who have their souls stolen by Dark Tails. And I Must Scream doesn't begin to describe it.
Episode 67: When Beelzebub attacks Chris and Cosmo and drags them into his lair, he seals Cosmo in a cage and then drags an unconscious Chris out of his chamber. What happensnext is fortunately not described. Then Beelzebub heals his ruptured internal organs, wipes his memory of the event, and throws him into Cosmo's cell still unconscious and naked. Cosmo is seconds away from the same fate when Tails finally reaches them. It's especially nightmarish for people who have suffered sexual assault, to the point where the author even has a trigger warning before the chapter.
Beelzebub later uses his stinger to torture the Chaotix. He sprays said acid all over Charmy, with predictable results.
Tails' Heroic Sacrifice is both this and a powerful Tear Jerker. Dark Tails attempts to possess him in a last-ditch attack. As Tails fights back with all his power, the Shroud parasite inside him - and then his body - begins to mutate from the Dark Chaos Energy surging through him. His bones slowly shatter one by one, his limbs turn to goo, and tentacles burst from his eye sockets as he tries to talk to Cosmo one last time. Eventually he stops talking when his jaw disintegrates, and then Cosmo finally kills them both with the Sonic Driver.
Magna Clades has a lot of these moments, but one in particular that really takes the cake is when the Big BadZoisite becomes a Blob Monster and liquifies the mayor of Beach City to death alongside many others!
The Les Misérables fic When The Cat's Away. Marius and Cosette being kidnapped by Thenardier and Patron Minette for their money, and Marius nearly being murdered is bad enough, but the most terrifying part is Cosette being tied to a bed and raped over and over by Montparnasse and Claquesous. They torture her, too - when Marius and Valjean arrive to save her, she's crying, bruised, and bloody. She specifically mentions Montparnasse sticking his knife under her fingernails when she tried to refuse him.
And then when the Kira Task Force (Matsuda, Aizawa, Ide, and Mogi) realize that Misa's missing and go to look for her, they search the woods and find her body hanging from a tree branch, with four other nooses tied neatly to the branch alongside her. Aizawa then gets a call from Near, who (while in so much pain he can barely speak) warns him that Kira has killed everyone in the SPK and is forcing him to call and tell the task force that he is coming for them next, before dying while still on the line. While they're all panicking, Matsuda realizes that the four other nooses are for them, and yells at the others to run. They don't even get out of sight of the tree when the Death Note takes effect, and the four of them are forced to slowly turn around and go back to the tree. They try to turn and run again, but they can't stop, escape, or even scream, and they are forced to hang themselves while terrified and still fully conscious. Matsuda's last thoughts before he is killed are "Please, Light, don't kill me, please don't - !"
Levi's ImagineSpots of all the ways childbirth could go wrong, including "Mikasa torn open from the inside and bleeding out, their baby coming out strangled on its own umbilical cord..." and of his child being Eaten Alive by a Titan.