The Masks We Wear seems to be heading this way, though unlike in canon the Fire Nation doesn't seem to have any intention of actually burning the continent down.
Lex Luthor grants Lois Lane an interview in Lex Luthor Triumphant 8 months after Superman vanished without a trace. We're told in 12 agonizing chapters how Superman is being dissected for science and profit, how his Fortress of Solitude is breached and seized, how Batman miscalculated Luthor's genius, how Wonder Woman and the JLA are duped into fatal scenarios and how, at the end, Lex Luthor ushers humanity into a golden age thanks to all the magic and science he took from the heroes.
The Pony POV Series has the Alternate Universe "Epilogue", which shows what would have happened had Discord succeeded in defeating the Mane Six. To say that it's a Crapsack World would a vast understatement. It's explored in more detail during the Dark World Arc of Season 6.
It turns out that Nightmare Eclipse wrenched control from Discord a long time ago and has been defeating the heroes and destroying the universe repeatedly ever sense. Ultimately subverted, however, since the heroes ultimately win.
The Axis Powers Hetalia fic Human Curiosity largely takes place about a hundred years after the villains win. The secretive HCS kidnapped most of the Nations, subjecting them over time in increasingly atrocious experiments. Many of the remaining Nations had given them up for dead.
In one of the most shocking twists in the entire story, The winner of Total Drama Stranded was none other than local Jerkass Calvin, though he was considered the better option when two of his fellow finalists were Keith and Chelsea.
Cupcakes itself: Not only does Pinkie get away with murdering Rainbow Dash, she takes Apple Bloom on as an apprentice and they work on Silver Spoon together. Note, however, others have written alternate endings, some where she does get her comeuppance after all.
Cheerilee's Garden: Sure, Cheerilee dies in the end, but she's never connected to the murders at all. In fact, she's seen as one of Twilight's victims, as the people blamed Twilight for everything.
My Little Avengers; although Loki dies at the end, he notes that his death will release a wave of magical energy that will mutate every living thing in the world within a few generations, creating the world ruled by magic that he always wanted.
In The CATverse, Batman isn't always around to save civilians from Gotham's supercriminals. This is played for Black Comedy in Tourist Trap and seriously in Small World. In both stories Crane abducts and tortures a victim into insanity without Batman or anyone else intervening or the victim getting away, and in the latter the victim is his younger sister.
In Ambition, Nightmare Moon, merged with Luna no longer, takes over Equestria. She has her hooves full though: creatures from another dimension are converging on her new kingdom, and the Princesses, Twilight, and her friends aren't out of the fight yet...
TeamRocket in Common Sense gets quite a few victories against Ash, such as successfully stealing the Moon Stone, a majority of the Pokémon at Pokémon Tech, the Squirtle Squad and a number of Pokémon from the passengers of the St. Anne.
The Evil Scintist, the Big Bad from Peter Chimaera's DIGIMON SAVEZ THE WROLD!!1111, successfully destroyed the road connecting an island to the mainland, essentially trapping people on the island. The narrative depressingly says that Digimon, the main character, couldn't do anything to solve this situation, causing him to go home and cry.
Pokémon Reset Bloodlines has Belladonna Tyrian, who enters the story with a goal to kill Tokiomi Borealis. She succeeds, albeit with (unknowingly) going against the same wishes she was trying to fulfill. However she does also gain something else during the act: the revelation of a possible half brother in Ash Ketchum.
Guardians, Wizards, and Kung-Fu Fighters has several examples of this in Chapter 9, as Hak Foo gets an Oni mask, Wong gets the Pig talisman, and Nerissa nabs the Dragon talisman, while the heroes walk away with nothing.