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.

Everypony knows Twilight Sparkle as the sweet, studious unicorn whose magic powers are matched only by her incredible focus and organizational skills. When Twilight's friends make fun of the way her checklists and schedules control her life, Twilight just laughs.

One day, for reasons known only to her, Twilight goes on an unstoppable organizing rampage. Soon, Rarity decides that she's had enough, and tries to stop Twilight before she organizes Carousel Boutique into oblivion.

Twilight Sparkle is very, very organized. Twilight Sparkle has never told anypony why she's so organized. Until now.

Ace was a street magician with a lucky streak. His luck was legendary among casino owners and fellow magicians. Any risky trick would succeed flawlessly and any gamble would pay off for him.

After performing his greatest and final trick he is brought face to face with the entity responsible for his incredible luck. The goddess of fortune herself. Lady Luck.

She offers him a deal. To become her champion, her Wild Card, and go to Equestria to spread luck among those who need it the most. So he finds himself in a magical land, in a new form, and ready for anything that comes at him. To a reasonable degree.

(Part of the Chess Game of the Gods universe created by Rust and BlackWing)
(Cover art by Grusborg on deviantART)

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

I always wanted to go to Equestria. When I got the chance, I took the deal without reading the fine print. To my surprise, I didn't arrive there as a pony, or even as a human. It seems I get to view this world from a different perspective than what I've imagined.

My name is Echo. I am a Diamond Dog.

-Edited by the one, the only, Nathan Traveler!
-(Cover by Jovial_Shake of fimfiction.net)
-Now featured on Equestriadaily.com!

Spiders. Oh, how I hate spiders. And yet Luna insists on keeping one as a...pet.

Just a little fun story to keep my skills sharp, so don't expect it to last very long!

Officially complete!

Trouble is brewing in Equestria, and Spider-Man is summoned to save the day! However, he takes the form of a pony upon his arrival and slowly starts to lose his powers. Now as Peter Pony Parker, he must become Equestria's new hero as the Amazing Spider-Mane, but with past failures haunting his mind, will somepony be able to give him the happiness he deserves and save him from a prophecy that ends with his death?

Across Equestria and through Earth, two hearts will join together, but one may die to ensure the survival of reality...

Cover image drawn by jmkplover and colored by Saljian

Official Theme Song done by XAVI- Playful Banter

It even has a Tvtropes page!

Spiders and Magic: Rise of Spider-Mane

Matt "MrBackpack" Mxxxxx has finally gotten his life on track; he's got a job that he loves, a good enough home, a beautiful fiance, and a dog. Little does he know that all of that hard work is about to be threatened by the presence of a very confused and very naked young woman appearing in his fudge-smelling Texas backyard.

Part of the PonyFall Collaboration series

It is the middle of the night when two bored princesses visit Twilight and her 'What If' machine. Join the three ponies and Spike as the view more:
Tales
of
Interest!

Pinkie Pie gets her friends to explain various aspects of Ponydom to the audience (aka a wall of Sugar Cube Corner's kitchen). A silly story poking fun at some of the fan-produced elements of MLP.