Finalist and judge's top choice in Equestria Daily's 2012 Nightmare Night contest.

Fluttershy has been plagued by nightmares, and Twilight wants to help her get rid of them. But when the bookish mare begins to pry into the depths of Fluttershy's unraveling psyche, she finds more questions than answers. What do her dreams mean? Why won't they stop haunting her? And why does the creature she keeps seeing inside them seem like more than just a simple night terror?

Let me tell you a story about the bad place.

Special thanks to Vimbert and Noble Jury.

With Mr. and Mrs. Cake away, Pinkie is left to take care of Pound and Pumpkin Cake, and she vows to be the best foalsitter she can possibly be for them. However, her plans are thwarted by something lurking in the shadows, something that has other ideas for the Cake twins...

An entry for the Nightmare Night 2012 competition.

In the back of the white marble archives, behind a rusted door, paint peeling and centipedes crawling under the frame, there's a set of stairs. They buckle like cork, and descend into a lightless library coated in dust, pages, and runes. Here, Twilight Sparkle stumbles upon a perfectly preserved body. Her own body.

Created for EqD's Nightmare Night Fanfiction Contest ~ 3rd Place Editor's Choice

Twilight is beyond the title protege. Prodigies are merely brilliant. Twilight has surpassed most of the greatest mages in history before the age of thirty. Twilight's research has changed the landscape itself. She is a living legend who some whisper may be the greatest user of magic to ever exist... perhaps even an equal one day to the semi-divine princesses.

But Twilight's knowledge is not infinite. She has one final lesson to learn. Twilight must learn the Final Law of Magic.

Daring Do cannot believe her luck when she is asked to help explore the most ancient tomb known to ponykind. But terrible danger awaits her, for beneath the earth rests something beyond equine understanding.

Warning: comments contain ending spoilers.

TVTropes page.
Alternate ending by Duplex Fields.
Archived in the Pony Fiction Vault.
Reviews:
One Man's Pony Ramblings
Louder Yay
PresentPerfect
The Royal Guard
Cleverpun's Critique Corner
The Goodfic Bin

A terrible accident leaves Sweetie Belle horribly disfigured. The once gorgeous filly is now deemed a freak, abandoned by her friends and even her sister. Thinking she's all alone in this cruel world, there is one who reaches out to her with the gift of friendship. The results turn out to be a little... chaotic.

This was my first fic. Pardon the crappiness.

"Applejack?"
"Yes Twi?"
"I found this book outside the Everfree Forest... It seems to be Apple Bloom's diary."
"Mah sis kept a Diary? Does it say what happened to her?"
"...Yes..."

TheLostNarrator did a fantastic reading of this story some time ago; find it here.
Now with a reading in Finnish, courtesy of DubbiKnight.
And a reading by Lotus Moon.

Twilight's relentless study of Pinkie's strange abilities leads to a horrifying revelation.

This site really needs an existential horror tag.

The following transcripts are of a journal found in Ponyville on April 16th of this year. The last recorded contact with the town had been 3 days prior, on the 13th, when a team under orders from Princess Celestia was sent to look into several missing pony reports in the area. When another group of investigators were sent on the 16th, the town was found deserted. The journal’s owner is believed to be the princess’s personal student, Twilight Sparkle. None of the town’s inhabitants have been located in the weeks since.

Readings:
Nimbus Productions
Scribbler Productions

I highly recommend both of them.

A print version of all the stories in this series can be found here. (There is currently a printing error I am working to correct. This will be available again soon.)