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.

She noticed the pony for the first time when she was young, not long after she'd received her cutie mark. He became her oldest friend.

Note: comments contain spoilers; please don't read them first!

Cover art by DaisyAzuras • Featured in the Royal Canterlot Library

Reading by Neighrator Pony • Spanish translation by Spaniard Kiwi

"It's called 'Shh'," said Fluttershy. "It's a game about who can be quiet the longest. Sound fun? I'm the world champion."

Fluttershy is not a pony who makes things up. She really is the world champion of "Shh," or The Quiet Game. And now it's time for her to defend her crown, with Twilight Sparkle and Rarity along for the ride.

Fluttershy's kindness to all creatures is legendary in Ponyville. When a freak storm blows in from the Everfree Forest, however, she and her friends discover the limits of compassion, and the dangers of living with your heart wide open to the world.

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

Twilight Sparkle flagrantly abuses her Come-To-Life spell, and learns a little bit about love in the process. Also, puns.

Now with actual cover art, thanks to the generous SuddenlyFerrets!

Now with a Spanish translation by Spaniard Kiwi!

She is as beautiful and graceful as the moon, and just as hard to reach. He is a young artist with much to learn about the world. When he accepts her challenge to create an artistic masterpiece, will he win her heart, or learn a terrible lesson in the nature of beauty and love?

Applebloom has had a room of her very own for over a year now, and she no longer has scary dreams when she's all alone in the dead of night. But something has come back to visit her, and this time she's old enough to know two things: it's not her friend, and it's not imaginary.

A very short and moody story about one of the many things grown-ups forget.

It's Mother's Day in Ponyville, and Dinky has a very special present for her mother.

Alone and far from Equestria lies a dragon; before him, a photograph of him and a mare he once loved. He remembers the moments they spent together, the moments that made him who he is, the moments that explain how he got here, and the moments that tell him where he is going.