First of the Savage Skies series.
After running afoul of timberwolves in the Everfree Forest, Fluttershy is saved by a mysterious young colt with a most unusual and disturbing feature. Realizing that he is alone, without anyone else to care for him, Fluttershy realizes that she must try to bring this lonely foal out of the forest and give him a life of love and friendship. The problem is that this colt's...unique qualities have made him more than a few enemies, including some who are closer to home than Fluttershy realizes.

Now with a sequel: The Promise of a New Day.
Now with a TV Tropes page.

It had been a year since Twilight had heard of anything from Trixie after the Alicorn Amulet incident. Unexpectedly, she receives a letter saying that her so called "rival" has tragically died and is requested to be at her funeral.

Thanks to CommanderX5 and Magic Man for editing.

Thanks to Neko-Me for the cover art.

Live Reading by Aria The Brony

While on her way home from a day with her friends, Apple Bloom runs into Twilight on a trip to Zecora's hut. After insisting to join her, little Apple Bloom gets lost in the woods after chasing a mysterious mare hiding amongst the poison joak. She stumbles upon a town completely isolated within the Ever Free Forest, but something about this town just doesn't feel right...

For as long as any of the Cutie Mark Crusaders can remember, Diamond Tiara had always been the biggest bully they knew. But when that said bully dies in an accident, each of them starts to go through their own emotional experience from this sudden change in their lives. Each will learn more about themselves and about the pony who they all thought they knew before she is laid to rest.

***Takes place just after season 3 but before season 4. This story is completed.***

Now with TV Tropes page

Princess Twilight sets up a war game for the Royal Canterlot and Crystal Empire guards. By kidnapping Luna and Cadance.

The guards thought she knew the rules. They thought she knew the guard manual backwards and forwards.

Sweetie Belle, Scootaloo, and Apple Bloom re-write the manual... and conquer Equestria.

Edited by Noble Thought.

Cover art: Princess Predicament by radiantrealm

One hundred percent approved by Twilight's Library (also approved by Discord).

Author Note: This is something new I wanted to try. Contains 10% human, 90% ponies, and 100% fun-filled, cuddlelicious goodness. Not suitable for those allergic to cuddles. Please consult your physician before reading.

A young university student suddenly finds himself thrown from his homework studies into a land filled with more colour than Gears Of War, talking ponies with ridiculously huge eyes, and topped with so many cuddles that it makes Care Bears look like Michael Myers.

And for some reason, all of them come to the conclusion that he must be smothered in cookies and cream-delicious cuddles.

For some, it's heaven; for Jamie, it's his own little plane of hell that makes even Satan feel torment.

Inspired by Forced Pony Cuddles

Yay! Thank you guys so much for getting this fic in the featured box! You all deserve huge amounts of cuddles. And you're gonna enjoy it!

Starswirl the Bearded is not used to dealing with fans, not surprising since he never had one before. But when a certain purple unicorn of the distant future discovers time traveling, Starswirl soon finds his comfortable days coming to an abrupt end.

Featured 7th Jul 2014! So much glory... what do I do with it all?
Chapter 1 of the sequel is out.

My name is Twilight Sparkle.
I am three hundred and seventy five years old.
Except for Spike, all my friends are dead...But not for long

Betrayed by Celestia, and isolated in her castle with only Spike for support, Twilight Sparkle enacts a powerful spell to reincarnate the element bearers through her own body.
Her friends will be reborn, and, with the trials of being a mother to her friends ahead of her, an unraveling secret from the past following her at every turn, and the possibility of a brand new life so close in reach, Twilight just might be reborn too.

Credit for both the inspiration for this story and cover picture go to
Crystal Leviathan

=====Originally Written February 2012===== EQD Post=====
After overwhelming Ponyville's mayor, the main six must fill in as she takes a much needed vacation. Yet, only one pony can take the title of mayor at one time. Which of our favorite ponies will be the first substitute mayor? How long will she be able to last before passing the job to somepony else? And in the end, will Ponyville survive long enough for its real mayor to return?

This story was written as a prize commission for the Smile Album Charity Event. The original prize was one by Stormy Seas and he provided the original premise for this story. He always wanted a story that could be shared and enjoyed by everyone, so be sure to thank him if you know him.

This story is a sequel to The Many Secret Origins of Scootaloo

When Scootaloo's attempt at flying causes her to crash into Twilight's lab, it sets off a chain reaction that causes Twilight to disappear, leaves the library in shambles and Scootaloo knocked out. A wave of purple energy rips through Equestria, leaving all to wonder 'great, what now?'

When Scootaloo awakens, she learns from the Bureau of Undoing Trouble from Twilight Sparkle that this world's Twilight is gone... and in her place are dozens of Twilights from different dimensions, tearing across the land. Worse, Nightfall Eclipse, a wicked Twilight from the antimatter universe, is assembling other bad Twilights to form The League of Evil Twilights, who seek to take over Equestria.

Now gifted with the ability to track down these Twilights, thanks to the explosion, Scootaloo will seek out these visitors from other universes in the hopes of sending them home and getting the real Twilight back.

Crisis of Infinite Twilights: Truth, Dare or Drink, the official spin-off, can be found here

Tvtropes Page can be found here

A listing of all the Twilights introduced so far (warning, SPOILERS) can be found here