WRITTEN BEFORE SEASON 5!!!
Without altering anything canon up to season 4 (though the movies are kind of skipped over, sorry), I manage to completely rewrite everything that happened. No, seriously. And it all started based off of Discord's photo-bomb in Fluttershy's window during the season 4 theme.

What if, rather than leaving with Celestia after he was reformed, Discord ended up staying at Fluttershy's house, unknown to any of the other ponies? Chaos ensues. (Pun intended. )

Definitely a Fluttercord.

This story is a sequel to The Monster of Canterlot

Peach Pit is a young earth pony that just joined the work force in Canterlot Castle. Unfortunately, she gets herself lost. Worse than that, she finds herself in the one place on the one day that nopony is allowed to be there. And she finds that she is not alone, for nopony is who she finds.

Oneshot based on The Monster of Canterlot.

Discord's the only creature in Equestria who can recognize the human for what he is -- not the long-lost Seventh Element that never actually existed and couldn't have existed before the human arrived, but a meta-reality warper, an entity far more powerful than Discord with the power to warp the minds of all around him and the very rules of magic to make sure that he's always the Big Hero. And the role the human's assigned to Discord is the Villain to beat down or kill.

Pre-reform Discord's fine with being the villain. But on his own terms. Not dancing on some alien interloper's puppet strings.

Without friendship, or even allies, Discord's going to have to find a way to defeat a creature who can alter fate itself and who can even mind-control him. Or he may just end up worse than dead.

Art by Tenchi-Outsuno. Progress Bar at my writing journal.

Trigger warnings: Mind control (magically induced love, magically induced friendship, magically induced stupidity, Discord being Discord), noncon/dubcon (magically induced love, other forms of highly dubious consent), rape (female on male), violence/gore (mostly against Discord), literally everything in chapters 19-21, humans not being presented as unilaterally wonderful and superior to ponies and/or draconequui.

The newly coronated Princess Twilight suffers an abrupt tragedy. Having lost two loved ones, she begins to question her own mortality, and that of her friends.

AJ, Dash, Rarity, Pinkie, Fluttershy. . . they are just the beginning. Twilight will live for thousands of years, so every pony she cares about—every pony she will ever care about, will die.

She could barely handle the pain of one funeral, let alone the thought of hundreds of them. Twilight finds a clever way to ensure all of her friends never die. They can’t all be ageless alicorns, but they can all move into Twilight’s Dollhouse. Then they can be best friends forever.

Sequel: Twilight's Dollhouse 2
Fanmade Song: Twilight's Dollhouse

Source: Dreampaw
Editor: Gage of Grandiloquence, Breath of Plagues
Pre-read & Idea pony: TypeWriterError,
v1.1 Revised chapters 1-10 on May 1st 2013
--Pending a few more revisions, including ch. 14
Now on TV Tropes.

Diamond Tiara's joy at her newfound outlook and friends is shortlived. Exiled to her bedroom while her uncompromising mother decides what to do with her, she can only listen in as Spoiled Rich tells her too-meek-by-half husband Filthy EXACTLY how useless his daughter is. Then, there's a sudden knock on the door... and Tiara's adventure is about to begin.
Set after the events of 'Crusaders Of The Lost Mark'.
Now rated T for some disturbing scenes
Beware of SPOILERS in the comments.
Great new cover drawn, completely at their own behest, by the very talented robsa990. What a nice chap he is.

This story is a sequel to The Monster of Canterlot

Sixteen years ago, the Lachances lost their only child in a flash, literally. What they didn't know was that their son Christopher was being cared for by Princess Celestia as if he was her own foal. Now, with Christopher's upcoming nuptials with Fluttershy, the family needed to be whole again. What could possibly go wrong?

When a six year old human boy is transported to Equestria by accident, he will need a home. Everyone needs shelter, protection and love to live a happy life, but who could love a predator from another world? Luckily for young Chris, somepony steps up to the plate.

Cover art by akumamattata Deviant Art
Re-imagined by Hunterhd1
Edited by Dream Seeker
Read by Leonexus Random

Searching for any records King Sombra may have left behind, Twilight learned of the shadowy king's tragic past. However, she also discovered his horn, in which his mind and remaining power were contained. Determined to learn how to use his Dark Magic for Good, Twilight brought Sombra back to Ponyville with her. After all, what could he possibly do as a horn? ...Or will he stay that way?

Edited by Darth Vendar and Myrkur
Inspired by Issue #1 of FIENDship is Magic
Gore tag just to be safe.

Edit 06/15/23: Now in the top 2K stories on the site, by rating! Thank you all!

When a joyful picnic at the beach celebrating Discord's TRUE reform takes a dark turn, The mane six are left with one question in mind, what was Discord's history? What pushed him to conquer Equestria single handedly? Unable to answer it, the ponies go to Celestia and Luna to learn of their friend's traumatizing origins