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Winter War takes the darkest elements of Bleach and runs with them. Bleach can get pretty violent, but it's usually contained in one-on-one duels, the only people who die are villains, and no matter how badly a good guy is hurt, they're unlikely to suffer any lasting consequences to it. Winter War throws that all out the window. Heroes die. Heroes will fight dishonorably or gang up on opponents if they have to. There are limits to what healers can do, and lingering injuries complicate daily life and battle alike. Aizen's Hollowfication experiments are shown as horrific and dehumanizing rather than being used as a source of power-ups. And the authors don't pull punches about the likely states of mind of people who've been on the front lines- or taken captive, or waiting back home for loved ones who are probably dead- for months.
Tiberium Wars manages to make the Command & Conquer Tiberium universe even darker than it already is, by virtue of introducing War Is Hell to show just how horrific the battles and weaponry in the setting really are.
Nick Fury Used to Be a Sweet Kid, being drinking buddies with Sirius Black and John Constantine and having acted as a big brother figure to Lily Potter for most of her life. By the time of the story, he is the epitome of Good Is Not Nice, proving to be a cold Manipulative Bastard whose personal Cynicism Catalyst was the death of Lily (they were so close that he was the second candidate for Harry's godfather and would have been godfather to the daughter Lily was pregnant with when she died - something he also may well have known, which is unlikely to have contributed positively to his mental state) - though it is unlikely that, as a muggle, being unable to take custody of Harry when he knew very well what Petunia was like, having Sirius, one of his best friends who he knew to be innocent, locked up in Azkaban and losing an eye to Lucius Malfoy.
Albus Dumbledore gives voice to his frustrations over the isolationism of the Wizarding World and the culturally enforced Medieval Stasis which strangles innovation and denied him the chance to communicate with brilliant non-wizards, save for working with Howard Stark during World War II, showing a brief glimpse of his dark side with frank admission that he remains capable of becoming a Dark Lord the likes of which Voldemort could never match.
Sean Cassidy is still a light hearted and wise Irishman (or Irish-American who's spent most of the last forty years living in Ireland and Scotland, as a compromise between the comics and the X-Men: First Class). However, as with canon, his wife was murdered by the IRA. His ensuing Roaring Rampage of Revenge was bad enough that parts of it still give Nick Fury, Director of SHIELD, former US Army Ranger and no wilting violet himself, nightmares over a decade later. Apparently it had something to do with Sean's Compelling Voice...
Johnny and Susan Storm's backstory. Their father murdered their mother when Johnny was six years old and it is more likely than not that Johnny saw it happen. After that, a relative took them in, then died, after which Sue mostly raised Johnny by herself.
Nick Fury notes that this happens to most SHIELD Agents, with the exception of Coulson, who manages to maintain his idealism and heart.
Carol Danvers is Younger than She Looks, being able to pass for a buxom college student at the age of 14 or so. This gains her a severe amount of unwanted attention.
Part 2 of Clash of the Elements. There is little to no humor, some rather grim scenarios are brought up during Smithy and Dimentio's (Fake) backstories, including Betrayal, paranoia and the strong pursuit of a dream leading to the death of Smithy's closest friend, Dimentio casually mocking the love of Blumiere and Lady Timpani, along with his fabricated story that mentioned a pregnant Daisy DYING during an alien invasion. And that's not even getting into Chapters 21-29...
The Discworld continuum offers the fanfics of A.A. Pessimal, which while written with a touch of Pratchett's absurdism, offer a darker edge to his fantasy world. The question from Pyramids, of what happens to luckless students who fail the Assassins' Guild School's Final Exam, is finally answered in detail that Pratchett only hinted at but did not give. According to reviews, this chapter moved one reader to tears. The Discworld country of "Rimwards Howondaland" is an expy of the old South Africa taken Up to Eleven, and has social institutions to match, as well as a paranoid and ruthless secret police - who are even called BOSS in the Discworld.
What makes this version of Freiza so terrifying is his motivation. In the original series, while monstrously cruel, Frieza's atrocities were mostly motivated by a desire to stay in power and to punish those who dared stand against him. In the abridged series however, it's made clear that Frieza commits his atrocities out of sheer boredom.
Alexandra Quick is this to Harry Potter, although in a way that doesn't go to the extremes of Darkfic or seem out of place with the mood of the original series. People do start dying in the first book though and there are some dark, dark plots in Wizarding America. Things get that way when you have wizards as government and wizards as terrorist with Blackand Grey Morality and you don't know which is which.
Let's not forget My Immortal, in which most of the characters have converted to Satanism "STANISM", Harry's scar is now a pentegram, and all the characters seem to do is Wangst around, cut their wrists, go to My Chemical Romance concerts, have sex, and proclaim how gothic "goffik" they are. The irony being that, for all its posturing, it's not nearly as dark as the actual later books of the series, for which see Literature below.
Hivefled; on one hand, the entire universe isn't being destroyed and nobody's mind-controlled or in thrall to an Eldritch Abomination. On the other hand, the plotline was kicked off by a series of events involving the Big Bad couple raping thousands of teenagers to death.
Horseshoes and Hand Grenades is set in the world of the friendship-based High School centered, Kamen Rider Fourze...except in this story, Gentaro was resurrected by an evil serpent and is causing mayhem as other Serpents start enacting Deal with the Devil themes with people who have died, more and more Kamen Riders get pulled into the madness, and at the end of the day, the bad guys are going to be claiming victory of some kind.
Game Theory is interesting in that while elements that were played for comedy in Magical Girl Lyrical Nanoha are now deconstructed for dramatic effect, and the lethality of the combat is notably higher, the characters are just as caring and morally upright as ever. In fact, the primary villain is more sympathetic. Which actually makes things worse,because Nanoha decides to help her. The ending , on the other hand, is actually happier than in canon. It just took a lot of effort and pain to get there.
Continuing with Nanoha fics, "Toward the World's End" starts out fairly light hearted with some cliche romance. It seems to just be so the author could get his OC with Nanoha... then, without WARNING, the entire world crumbles to dust and the only known survivors are Nanoha and Arthur, the OC of the author. Explicitly mentioned are the deaths of Arthur's mother and best friend, of Nanoha's childhood friends Suzaka and Arisa, and of course, Yuuno. Nanoha and Arthur wind up on a deserted island (Because these too many corpses of humans everywhere else) and are resigned to a hopeless life. At the end of the first story they bet their lives, not caring about the outcome, on a tiny Hope Spot.
It's back to being a fair bit lighter in the following fics - however, the "everyone's dead" deal is still in effect
The story, Shell Shock is an incredibly dark take on military stories in the My Little Pony: Friendship Is Magic fandom. It actually warns the reader: "This is seriously the darkest thing I have yet written. You have been warned."
The Vinyl And Octavia Series is a fairly lighthearted comedy series...until Vinyl and Octavia in 'Dial D for Detectives' , which features the two investigating a murder. It only gets worse with Vinyl and Octavia Duel Destiny, which ends with the two going to prison and with the villain getting away scott-free. That being said, the two aforementioned stories are only dark in comparison with the rest of the series - they both still have a decent amount of comedy in them.
For a show as innocuous as My Little Pony: Friendship Is Magic, there is quite a substantial amount of fan media with this in mind. Indeed, a great deal of the fanfiction is darker and edgier to some extent due to addressing more mature themes than the show. This is, of course, disregarding the stuff which is MUCH darker:
One of the most notable examples is Cupcakes, a fan fiction that has gained memetic status within the Brony community for its rather horrifying portrayal of Pinkie Pie and her cupcake recipe.
Another infamous one would be "The Rainbow Factory". The song it was based upon insinuated that pegasi did something to make pretty rainbows, but what, exactly, was left to the imagination. The fic spelled out in explicit detail the murder of foals too weak to fly.
Yet another example is Cheerilee's Garden, where Cheerilee deals with unruly students and the mane 6 (in the sequel) using certain methods. Arguably far more bothersome than Cupcakes, which may be why less people have read it.
The fanfic series RainbowDoubleDash's Lunaverse. It begins with a mild case of this, where the evil alicorn (here Corona, not Nightmare Moon) is able to remain free after being hit by the Elements and continues plotting to conquer Equestria. This amplifies over the course of the series, to the point where the season finale set at the Gala — in contrast to the original show, where the gala story was just about the six friends showing up and making a mess — has the Lunaverse 6 basically conducting a sting operation in order to get a known criminal arrested, so that she can spill the beans on the nobles of Equestria, who vary from apathetic to outright corrupt.
Dusk's Dangerous Game features centuries-length plans for breeding more alicorns, including deaths of mothers through birth, and a full fledged uprising... all fueled by best intentions of a control freak. She gets better... Nah, not really, but she has to gulp the will of Deus Ex Machina.
The fanfic The Monster We Made is this trope. The story chronicles the last thoughts and actions of everypony as they are put to death by Alicorn Twilight Sparkle
The premise of People Lie is that Naruto was deeply affected by an act of violence during his youth, one that transforms him into a manipulative person with little interest in friendship. A running theme of the fic is how "some characters may have turned out even worse off if they had a father or mentor to look up to".
Evangelion 303: This doujinshi makes this by aiming for realism. It removes the Evas, Angels or Adam or Lilith, uses real world politics in the setting and changes the main characters' traumas for different psychological issues.
New World. A nice story about a teenaged boy and his adventures with pokemon, that just happens to feature murder, rape, and the apocalypse. The very first chapter features a Scyther beheading another Pokemon and then then being horrifically and disgustingly killed.
The Pokémon anime has taken on a much darker edge with Cornova's Poké Wars. Where the stories are set, all the regions have been ravaged by war. Not to mention, the stories are much more violent, cynical, grittier and much less idealistic than the anime it was based on.
Pokémon has gotten a makeover with the advent of The Sun Soul, which combines a pointed Deconstruction with an Anyone Can Die attitude. So far, if the reviews and forum opinions are to be believed, the fandom approves.
Twilight Pretty Cure, is a milder example. There's no blood or violence, but it will explore lots of serious issues like bullying, discrimination, child abuse, and thick tensions between friends when things don't go right.
Angel Island Zone. A retelling of the events of Sonic 3 from Knuckles' end of things. More blood, more tears, more drama, and more character development. And surprisingly, it manages to pull it off quite well.
Prison Island Break makes most attempts at Sonic the HedgehogDark Fic look like a cookbook, taking the best part of the franchise to prison. And this baby ain't based on the mistaken identity event that you saw in Sonic Adventure 2. We're talking Sonic the Cop Killer. It's not just the rape, the multiple murders, the sadistic Head Warden or the way that the writer seems to find a new way to violate basic human rights in every chapter. It's the way they give the readers the gut-churning feeling that they actually Did Do The Research.
Sonic X: Dark Chaos is a full remake and Deconstruction Fic of the third season of Sonic X. While the original season was quite dark on its own for a Sonic the Hedgehog series, this fic takes the grim elements to the extreme. The galaxy is a war-torn Crapsack World ruled by demons and infested with Shroud parasites, graphic violence and Nightmare Fuel abound, numerous characters die, and the ending is bittersweet at best and full non-comedic Shaggy Dog Story at worst. And the rewrite is often even darker that the original, featuring such pleasent themes as near-galactic destruction, cannibalism, horrific science experiments, fundamentalism, religiously-forced pregnancy, and male-on-male demon pedophilia.
Team Fortress 2 is normally quite a violent game, but always in a light-hearted and comedic way. Respawn Of The Dead, on the other hand, is brutal and disturbing in its violence and very, very dark. Cat Bountry takes the personal quirks of the characters and expands them into full-blown psychosis. The result is actually quite good.
Cuanta Vida has moments of this as well, although in a very different way, largely by actually confronting some of the inherent Fridge Horror of the premise of the games. The fact that the characters are actually somewhat toned down from their portrayal in-game somehow only makes it worse. (For example, in the game, Spies are backstabbing bastards who relish killing. The main character spy, Bleu, actively avoids it.)
Special mention should go to the "Rotten Dirty Bastard" fics. The special was Black Comedy dedicated to going to extreme lengths describing how much The Nostalgia Critic makes everyone's lives suck. The fics will either point out the flaws in these "happier lives" (like Iron Liz never meeting Linkara as one example) or have this heartbreaking sense of loss that makes you want to cry.
The Legend of Total Drama Island, a reimagining of the show's first season, achieves this effect by several methods, most notably by playing for drama certain incidents that the original played for laughs, and by replacing certain cartoonish elements of the original with some pretty stark realism.
Cenotaph zig-zags this trope as both played straight and inverted. On one hand Taylor's father is murdered by Bakuda on the other, Taylor dosen't spend the first month of her cape carreer fighting for her life against both sides of the law.
Fallen King shows what could have happened if Yugi lost to Pegasus, it deconstructs the power of friendship that the series runs on. Joey realizes that the villains can and will use it as a weapon, and ultimately decides he, Tristan, and Tea must stop being friends to save the world.
Pikachu gets made into a coat by Team Rocket, causing Ash to kill himself, Mary Poppins gets hit by an airplane while flying with her umbrella, Alice accidentally poisons herself when she drinks from the "Drink Me" bottle, just to name a few of the fates of famous popular characters in stories by Hans Von Hozel.