It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

What if Discord had not been turned to stone by the Mane 6? What if he had escaped?
It is three years later and the Mane 6 have moved on with their lives, all except Fluttershy, who cannot get the draconequus out of her mind. The others are happy in their new and comfortable lives, until their enemy returns and will only relieve Equestria of his havoc in exchange for a bride.

This has been adapted into an audio series.

Also, here's a dramatic reading by Pablo Didonna, and one by 666HellGirl1

Cover Art by Nstone53

French: http://www.deviantart.com/art/Une-Mariee-pour-Discord-La-fuite-440318295
Spanish: https://www.fanfiction.net/s/10203187/1/La-Novia-de-Discord

*Bronyland Pony Awards Nominee 2013

This story is a sequel to Discordant

Almost ten years have passed since Scootaloo helped free Discord. She’s learned to live with the consequences, but it’s never easy. After being fired from the local weather control team, she receives a letter from Princess Celestia, offering her a job as an assistant flight instructor for gifted pegasi. With no better options, she reluctantly accepts. But why her, what game is Celestia playing, and what exactly is going on in Canterlot?

When Twilight Sparkle slipped beneath the covers last night, everything had been fine. She had friends whom she loved, a teacher she adored, and a bright future ahead of her. But when she woke up, her blankets and quilts had been replaced by hospital gowns and padded restraints.

Everything is wrong and nothing makes sense; even her friends have changed. The doctors keep telling her that she is sick, that none of it was real and that it was all in her head. Yet she remembers a life far beyond the hospital walls. She couldn't have made it all up on her own. They must be lying… right?

Ask Asylum Twilight - Still updating regularly!
Equestria Daily
TVTropes
Asylum Fan Group
The Tartarus Project
Russian Translation
The Asylum 20,000 View Spectacular Stage Show!

Art:
Asylum Cover by conicer
Twilight and Twilight Smiles by dreamingnoctis
Mirror Twilight and Plague Doctor by Jaestring / BloodGoldWings
Twilight Smiles and Doctor AJ by conicer
Nurse Ratchet and Silas and What's in the mirror? by Archonix
Doctor AJ Sketch by Archonix | Colored and vectored version by ReFro82
Twilight's Asylum by Khan the Cake Lover
Smilight by HappySwitch
Twilight Waking Up by Dombrus
Fan Art by toxicdemon10
Asylum Twilight by Madness-With-Reason
Asylum Fluttershy and Asylum Ch 26 by Downburst-Backspace
Twilight and her Twin by v747
Birdgirl by sirValter

Readings and Videos:
Asylum Animated Trailer Video by formuladash
Reading by Gammarobot (SugarCubeRadio): All Chapters Here
Reading by Ender Brony: All Chapters Here
Reading by VisualPony: All Chapters Here
Reading by MelancholyIguana: All Chapters Here
Fan Trailer by Kaidan: Asylum FanFic Trailer Cuckoo's Nest

Sanctuary by Kaidan
Broadhoof Files: Dr. Humors by TypewriterError
Broadhoof Files: Corporal Phalanx Spear (Ret.) by Phalanx Spear
A Hearth's Warming Tragedy by Seven Fates

A special thanks to Breath of Plagues, Rex Ivan,
ChudoJogurt, Cynewulf, Death the Kid, Selbi, PrinceDolph, Blahman2816, Queue, and Gage!

Axan Zenith - Dr. Dreamer
Dratini4 - Way Finder
psychicscubadiver - Bright Mind
Velkaden - Dream Chaser
Reese - Silver Glow
Viola Heartstrings - Clover
Archonix - Spinney Whiteacre

Diamond Tiara has always enjoyed picking on the Cutie Mark Crusaders. But one day, she finds she's gone too far, and everything for her comes tumbling down. But help may come from the most unexpected of places...

Started before season four, and does not take season four canon into account.

This story is 100% Diamond Cutters Approved!
Note: If reading this inspires you to write your own Diamond Tiara fanfics with similar premises, send me a link, as I'd love to see them.

Hearth's Warming Eve has come once again, which means fun in the snow, warm food, and spending time with family. At least, that's what it means for most ponies. For Scootaloo it means a day off from crusading, loneliness, and the coldest night of the year. When Discord begins to whisper to her from his stone prison, she questions the beliefs held by many. What was so great about Harmony? What could be so bad about a world where chocolate milk fell from the sky?

Thanks to The Band Brony, Gsppcrocks10, Inkscrawler, TheBuggiest, and minjask6572 for help with editing. Thanks to SStwins for the awesome cover art.

Now with its own TV Tropes Page!