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.

This story is a sequel to Entrenchment

An Age of Iron story.

At last, Ferrous Dominus is (mostly) secure.
Centaur III has been (largely) pacified.
The enemies of Chaos and Equestria have finally been crushed (probably).

But victory is merely a prelude to the next war. The Imperium of Man and the pitiful, far-flung holdings of the alien await the Iron Warriors and their new allies, ripe for conquest and plunder. With a new home world and a new ally under their thumb, the 38th Company at last turns its attention on a galaxy ablaze with constant war, seeking new victims to fill the bellies of their ships. The gentle but resourceful equines of Equestria travel with them, taking to the field not out of malice or avarice but gratitude in at last fulfilling their grave debt to the Legion.

But in the depths of the void, far beyond the fleet, beyond the veil of the Materium itself, Chaos is not idle. Plots advance, blood spills, and ancient evils seethe.

The light will be extinguished.

(Dark humor warning; grimdark themes)
(Cover art, and pretty much the rest of the art too, by EZTP)

Sunset Shimmer has always been a hot-headed, impetuous girl. She's always been prone to making snap decisions, and later finding herself regretting them. It was exactly this temperament that had brought her to the human world, penniless and alone. When the opportunity to get back on her feet presented itself in the form of a stranger's outstretched hand, she leaped at the chance.

This is the story of a woman who has made many bad choices, and the life those choices have made for her.

Tags, and even rating, may change as the story goes on.

Thanks as usual to Magello for the cover art!

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!)

This story is a sequel to Iron Hearts: Book 5 - Suffer Not the Alien to Live

An Age of Iron story.

Months have passed since the destruction of the Ork Space Hulk and the end of the war against the Waaagh that threatened to swallow the Centaur system and all its inhabitants.
The Iron Warriors' 38th Company is the absolute military power on the planet, and the survivors of the Lamman Sept and the ponies of Equestria stand with this mighty army of Chaos as they claim Centaur III as their own. Although the other nations of their world may not fully recognize the Company's dominance, it is no matter; the Iron Warriors make plans to return their cargo to the Eye of Terror and return to their eternal trade of piracy. The planet is secure, and can be shrouded by Warp storms at their whim. The natives are divided, weak, and anyway occupied fighting off the scattered Ork warbands. The military supremacy of Chaos is unchallenged, and bolstered by Equestria's reluctant, but hard-earned support.
As Ferrous Dominus expands its operations and the fleet performs its long-suffered duty, it seems nothing can stop the Iron Warriors and their equine allies. The denizens of this conflicted world start to hope that at last peace - if not a distinctly unstable and militaristic peace - has come, and they might start constructing a new, better future from the ruins of war.
But hope... is the first step on the road to disappointment.

(Dark humor warning; limited grimdark themes)
(Cover art by EZTP)
(Featured on 9/19/2015)

Unhappy that her future as a member of the monarchy is denied by Celestia, Sunset Shimmer escapes through Starswirl's mirror into another world, planning to take it over to prove once and for all she was fit to rule. What she didn't expect—besides a species change—was to arrive in a world already conquered.

TvTropes Page (Just created! Needs Help!)

Art (Will contain spoilers)

Sunset Shimmer - Bloody Sunset

Spoilers Ch. 11+: Angel - Angel and Sunny
Spoilers Ch. 18+: Princess - Comic
Spoilers Ch. 121+: Alejandra Acevedo - Flying at the speed of death
Spoilers Ch. 161+: Apple Bloom - Bloom
Spoilers Ch. 180+: Food - Sunset's Party Dress
Spoilers Ch. 185+: Fugue - Fugue by Rametep
Spoilers Ch. 197+: Exhausted

(Art is always welcome!)

WARNING: CONTAINS SPOILERS FOR THE WHOLE STORY: TIMELINE