Twilight Sparkle goes to the Apple Family farm to retrieve Smarty Pants from Big Macintosh, and realizes that she may have done some damage to him. Concerned for his well-being, Twilight Sparkle works to ween him off his new condition, and consults with an expert on the subject. Over the following weeks, she realizes how troublesome taking care of anypony can be a hassle.

Pic by Egophiliac on DeviantArt
http://egophiliac.deviantart.com/art/snuggles-263525715

Derpy Hooves is secretly a changeling.

Nopony particularly notices, or cares.

(New 9/15/19: Spanish translation by Spaniard Kiwi! Thank you!)

When Twilight Sparkle invites Applejack and her little sister to lunch with her and the rest of her friends, Apple Bloom is thrilled to be joining the mares on a grownup lunch. She resolves to get Twilight Sparkle a gift to thank her for her thoughtfulness. This gift serves two purposes though, and it's not until much later that Applejack discovers that Apple Bloom was setting up Twilight Sparkle and Applejack to become marefriends from the very beginning.

Warning: Third-person limited with multiple POVs. This is a shipping fic with the Applejack and Twilight pairing.

EDIT: Added the 'Sex' tag because there are a few implications, though no physical descriptions.

The erogenous 3rd edition. It's 30 percent longer, 300 percent better edited, 3000 percent more ethically dubious, and still narrated by Steven Fry.

It's that special time of the month again for the Elements of Harmony; the time when they get together for a Truth or Dare game of a more questionably pure nature. From long kept secrets, to reflecting on parties they can barely remember, their three years of friendship have changed them. For better or worse, they were still deciding on that.

This game will be different. Most likely for the worse, but that's what drinking before the sun sets can do. Or maybe them being hornier than usual. Or secretly planning each others sex lives. Or falling in love with each other. Or all four. Most likely all four.

Twilight wants to go out on her first date, but will alcohol and the raunchy advice of her friends help? Rainbow badly wishes to sedate her loins, or maybe she's looking for something more? What exactly, is Rarity planning for this night? Should they really add weed to the equation?

The Elements all have desires they haven't quite realized they have had, and a day long exchange of sex jokes and tension might lead to events that are out of their control. It was in their control once.

Our innocent little ponies seem to have sucked in too much Seth Rogen, but that's okay.

Right?...

It's Archer with ponies.

A certain pony has a problem: She has long wished to be the Apple of Flutter's eye. One day the pegasus herself wants to come over and Applejack opens the door to find her crush holding flowers! Is her luck finally changing?

Twilight Sparkle has hit a wall in her studies. So when she is tasked by Princess Celestia with joining an expedition on a faraway island, she can't help but see it as a form of punishment. Nevertheless, she packs her bags and heads to Baltimare, one of Equestria's many port cities. It should have been simple: find a ship offering passage and pay them to take her to Haven. She soon learns, though, that ponies are afraid of the unknown waters past Eternity's Crossing. Despite her best efforts, she is unable to find a ship willing to take her there. That is, until she meets Captain Rainbow Dash.

Brash and enigmatic, Rainbow Dash, along with her crew, are the only ones willing to ferry Twilight on the waters of the Forgotten Sea. She expects six months of quiet travel that will allow her to continue her studies. What she gets is an adventure which makes her realize that, when sailing the high seas, the line between right and wrong is never as clear as it seems.

(Featured on EQD as of 4/28/13
A huge thanks to Breath of Plagues and Amacita, who are amazing editors.
Credit is also due to psychicscubadiver and Zeta040 for pre-reading.)

Awake and alone, Applejack will find a way to survive.

And here's a TV Tropes page, if you're into that kind of thing.

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

This story is a sequel to Ascend

Congratulations, Twilight. With Celestia and Luna on their constitutionally mandated vacation, you're in charge of Equestria. The position of Regent is an honored and hallowed one. But maybe it's a bit early to congratulate you. After all, whether it's a nobility jealous of your ascension, or a military unhappy with Celestia's decisions; one thing's certain: your reign will be anything but peaceful.

Cheer up, Twilight. It's not every day somepony changes species. In fact, no pony has ever changed species. It's something new and you like discovering new things. Granted, Equestrians don't like new things, especially things that fundamentally alter their government. So maybe there is reason not to be happy after all.