Now Featured on Equestria Daily!
TV Tropes and a group of its own.
Audio version
( EPUB / MOBI )
Three Nights in Manehattan, a sequel
Hardcover Print-on-Demand Order Page

As a child, Daphne knew of a world where magic lived, where an immortal princess reigned over a beautiful kingdom, and longed to journey there beside Leit Motif, the filly she'd grown to love in the woods behind her home. But one day, when she needed her most, Leit Motif was gone, and she never came back to show her the way. As she grew, she put aside her childish dreams, and taught herself to believe the lie.
When forces beyond her knowing take her sister Amelia, though, she discovers that her childhood fancies were entirely too real, and is thrust into a journey that will take her back to that land she longed for, back to the childhood friend she'd abandoned, and to worlds she'd only dreamed of.

Interview with Pre-Reader Amacita
PresentPerfect's Review

Sam Horner's life hangs in the balance as a mysterious illness slowly weakens him. While his parents are preparing to say goodbye to their son, a mysterious benefactor shows up in Sam's dreamscapes, which resemble locations from My Little Pony: Friendship is Magic. Notable locations include Ponyville, the Everfree Forest, and Zecora's hut. Will Sam recover completly and become something different?
Special Thanks to zeusdemigod131 (Zecora), who will be providing Zecora's role in this story.

Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Beautiful, gifted, and faithful student of the Princess of the Sun, Siren Song has very nearly everything a pony could want. Sometimes though, in the twilight hours, Siren can see the sadness in her mentor's eyes. Once, ponies whisper, the Princess had another student named Twilight Sparkle, but she left Equestria, never to return. The pony who has a perfect life just needs one more thing—to convince Twilight Sparkle to come home so the Princess will smile again. But when Siren arrives in pursuit of Twilight, she soon finds herself trapped in a city of horrors, with only its monstrous denizens for help.

Now with a TV Tropes page!

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

What does Rarity have in common with a werewolf, a vampire, a tall computer specialist, a psychic reformed redneck, and a foul-mouthed wizard? Well, at the moment they're all human. And saving the world.

Editing by Northwest Brony and Suke

This story is a sequel to Pony Age: Origins

With the defeat of the Archdemon, Twilight Sparkle, new Arlessa of Amarethine, must assemble a new team of Grey Wardens to defeat the threat of the ponyspawn. Her friendships will be challenged by a cunning new foe while betrayal and deception lurks behind every corner.

The Ponyspawn have invaded Equestria, and it is up to the newest addition to the Grey Wardens, Twilight Sparkle, to find the means to drive them back! With her friends and allies at her side, can Twilight defeat the evil tide before all of Equestria is devoured?

The Sequel, Pony Age: Catalyst, is available.

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

Inspired by the heroics of the mysterious mare known as the Stable Dweller, Silver Storm, a guard of the town of Marefort, decides to go on a daring mission to rescue her captured brother. Of course things rarely go as planned and her attempts at heroism drags her into a tangled web of plots and conspiracies as warring factions vie for control over the last great city: Dise.

Spanish Version translated by Spaniard-Kiwi: https://www.deviantart.com/spaniard-kiwi/art/Fallout-Ecuestria-Heroes-996263393