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.

There was only one explanation. For all of it. All of the strange, erratic behavior. Her irrational fear of the sun. Her nocturnal habits of locking herself in in the dark and closing all the blinds. Wearing her sunglasses everywhere, even inside! It was time to invest in some silver, garlic, and a wooden stake.

It is Hearth Warming Eve time and a tragic, sewer dwelling, Pegasus born with bat wings and a set of sharp teeth named Fluttershy Cobblewing AKA The Pegabat is planning to return to normal society after a lifetime living in the fringes of society which included a time being a sideshow freak at the circus and as a prisoner in a lab owned by the ghoulish and sadistic Crystal Emperor Sombra. Fueled by her cruel and horrific backstory she desperately longs to be accepted into society as a fellow pony not as a freakish monster at all costs. In order to achieve this she teams up with corrupt businesscolt Filthy Rich who wants to rule the city with The Pegabat as his puppet mayor by unleashing a horrific crime wave on citizens of Ponyville. But Ponyville's superhero Mare Do Well AKA Princess Twilight Sparkle is the only one who can stop The Pegabat and Filthy Rich's scheme. Based on Tim Burton's Batman Returns and Elfen Lied.

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

This story is a sequel to Bride of Discord

Discord and Fluttershy are blessed with a daughter named Screwball, who is gifted with incredible power that attracts the attention of the Queen of the Changelings...as well as her son.
When disaster strikes that tears Screwball's family apart, it is up to her to bring it together again.

New cover art by floppy-fluttercord

Rarity's family name is in shambles, and her fortune is nonexistent. To return what her father squandered, she and her good friend Pinkie Pie turn to piracy, commandeering a magical airship and kidnapping the princess's personal student.

When Princess Celestia learns of Twilight and Applejack's abduction, she doesn't agree to pay the ransom. No, she hires the sky's greatest tactical mind, the Daring Swordspony Rainbow Dash, and her sidekick, Fluttershy. As the two groups engage in a game of cat and mouse, more dangerous threats hang on the horizon. Aztec Curses, angry gods, and a mysterious figure known only as the Derp Pirate Roberts.

Will the six Elements of Harmony be able to gather the seven pieces of eight, or will the world fall to utter chaos, and rise up as an empire of anarchy and piracy?

Now with its own TV Tropes page thanks to Cleverpun: TV Tropes

I don't know why I'm even keeping this thing. Who the hay's gonna read this and who the hay would even care?

Being dead sucks.

Based on the awesome Ask Ghostly Scootaloo by RoseXKnight. Please if you enjoy this fic check them out. Characters used with permission.

No extra characters, events or abilities added by me are canon unless otherwise shown to be so on the blog itself.

For an extension of this canon check out Ask Kuleco (warning spoilers for Diary of Ghostly Scootaloo, Ask Ghostly Scootaloo and Rainbow Factory).

This story is a sequel to Monsters

You might think that Equestrian nights are but serene exhibitions of Luna's work on the sky. You may believe that you can just lay out on the grass and admire the beautiful stars as a warm evening breeze caresses your mane. And you would be wrong.

Equestria is a magical place, and where there is magic, there is chaos. Dead rising from their graves, inanimate objects coming to life, strange apparitions making your foal cry in her room... sounds familiar? No? Then I'm doing my job right.

I'm Twilight Sparkle, and I work the Night Shift.

This follows canon up to the end of season 2.
Check out the Fanart Repository for lots of awesome Night Shift art!

Featured on Equestria Daily.
Winner of Stories Back from the Read 2013.
One hundred percent approved by Twilight's Library!
Special thanks to Nonagon and Wise Cracker.

[Psychological Grimdark]

This story was directly based off 'Awoken': Wooden Toaster and H8 seed's spirited successor to the Rainbow Factory.

Food for thought, folks. I wrote this story on my own time and Obab later added extra material, three years later, when she converted the story into her audio production. She did not participate in the original production (if that was not clear already). If you read the story below you'll see the original, untampered text!

***

The decline into darkness had been easy enough... but when a high ranking Rainbow Factory employee begins to loose faith in the program and attempts to leave, things get out of hoof.

Having lived the majority of his life in the twisted building known as the Rainbow Factory-climbing up the brutal ladder and eventually becoming an Orchestrator-a lone colt finds the atrocity's he's committed in his past coming back to haunt him in his waking hours.

Driven by the need to return to normal society and the thought of redemption, he devises a risky plan that will ultimately decide the very fate of the Rainbow Factory as it's come to be known.

***
A long list of special thanks and mentions...

Thanks to Aurora Dawn for essentially creating the world I based this story in.

Thanks to Wooden Toaster and H8 Seed for the awesome song
Thanks to Fiasko0 on Deviant art for making the picture for the song (which I snatched)
Thanks to xzenocrimzie (Starlight Sparkle) for working with me to get the story out and into public
Thanks to wandered D for the tech support (he knows what I'm talking about)
Thanks to SrPeachFuzz on YouTube for accidentally bringing the story to everyone's attention
Thanks to my brony friend Josh for helping me get the story from my head, and into an outline
Thanks to both Truesoul116 and OhOhJackarias on YouTube for their excellent readings
Most importantly, every brony out there that has read, liked, faved or commented! Without you all, this would of never happened!

*Audio books are up!

Another really great dramatic reading!

If you're looking for a dramatic reading

If you're looking for a clear and professional reading

All three of these readers were totally awesome! Thanks guys.

Now translated into:
Polish by Dolar84
Spanish by Moonlight Fan

This story is a sequel to Rainbow Factory

Cloudsdale Weather Corporation has been running without incident for over twenty years. That is, until two foals manage to avoid being processed and find themselves in the haunted bowels of the massive facility. Can they make it out of the abandoned factory with their sanity intact? Will they uncover the secrets even a company as dark as the CWC is ashamed to keep? And what of the workers who help ensure that, in the end, not a single soul gets through...

Love the series? Buy the book!

—[TVTropes Article]—[Plagen Shiki's Reading]—[The Song Inspired by the Story]—