Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

After years on the road, Twilight Sparkle and Spike pack up their lives again.

One by one, Twilight and her friends must come to terms with the consequences of being the Elements of Harmony.

These stories take place in the intervening time between Season One and Season Two,
with the exception of Ditzy Doo: Muffins, which takes place early in Season One.

The series continues in the sequel, Secrets and Lies.

Pony Psychology has a TV Tropes Page.

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.

After being saved one day by Rainbow Dash, Silver Spoon develops a crush on the number one flyer of Ponyville. Needless to say, a certain Pegasus filly isn't too pleased with this.

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 But when she woke up, her blankets and quilts had been replaced by hospital gowns and padded restraints.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

One would think that the wounded Trixie would appreciate Twilight Sparkle taking her in to nurse her back to health. But for some ponies, leaning on someone else isn't so easy. Their crossing of paths sets them both on a journey that neither of them would've expected...

After being rejected by Rarity, Spike falls into a state of depression. There he becomes friends with an unlikely pony, Diamond Tiara. As they become better friends, Spike finds himself drawn to Diamond Tiara in more sinister ways.

Spike x Diamond Tiara ship. No foalcon.
Officially approved by the Diamond Cutters!

Rarity has a secret. Well, two secrets. First, she has a crush on one particular pony. And second, she has been writing a story for the object of her affections, to reveal her love. But when word gets out about her literary abilities, suddenly all of her friends want her help on their own writing projects. And all of them need to be done by Hearts and Hooves Day! Could Rarity not be the only one with a hidden agenda here? And how exactly will she manage so many projects in such a short period of time?

(Updated with some editing help from the superb Exuno)

~A simple tale told through the format of letters~

It's just a date, right? What could possibly go wrong? But when the scientifically-minded Twilight Sparkle deems it necessary to start writing letters to Pinkie Pie about it, bad approaches lead to misunderstood intentions, and it's up to Twilight to solve the problem herself.