Octavia has hit rock bottom. After the Gala and being forced to play that song, she was cast out by high society. Now she must gather the shreds of her pride, only to have to swallow them to work under the only pony that seems willing to hire her. Now it's time for her to make a name for herself all over again, and she's determined to make it no matter what, even if she has to start over from Scratch.

(Second Person Story)
You are a human who has found himself in Equestria. As if that wasn't bad enough, you're not quite as tall as you were when you started, and not only have to survive at a greatly reduced size, but then you have to live with it. Of course, Equestria is a place where there's always somepony willing to lend a helping hoof, and so you never lack for support. But what can they do for you really, if they can't make you bigger, or get you home? As the tale goes farther, you begin to question if you even want to go home, and then the ultimate question is asked; Can you earn your happy ending? Read and find out.

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

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.

There is a world where Life and Death govern all imaginable realms. A world where Watchers guard over their planets and the creatures that roam them. In this world, a young soul goes on a journey to a place he never thought existed, after cutting an untold deal with Death.

Equestria, a place of magical creatures and mysteries, offers him a new chance at life. A chance he will have to pay dearly for. This is the written story of his adventures, some of the sorrows and victories of his life as he goes through great challenges and fights his inner darkness.

At the end of this journey, one begs the question: What is better? To be born good, or to overcome your evil side through great effort and sacrifice?

Tagged with Human for the prologue.

Follows show's cannon up until end of Season 2.

Now a published book!
And it's own TvTopes page!

Spanish translation: Here

First chapter published January 2012
Marked as Complete on 31st August 2014
Published (printed) on 25th November 2014

PM me for the full digital version of the now-printed book! (includes text PDF, full cover and fan art)

Nightmare Moon has won, and the world has been shrouded in eternal night. But hope still lives. The land of Equestria is currently divided between the armies of the usurper and those of the Dawn Militia. However, the greatest danger to the rebellion may not be the dreaded Mare of the Moon, but her lieutenant, Eclipse–formerly known as Twilight Sparkle.

Caught in the middle of a struggle between Equestria and a neighboring country, Blueblood finds himself alone in unfriendly territory. Through trials and hardships he finds himself under the wing of a veteran soldier, and the arrogant, spoiled stallion begins a slow metamorphosis into the prince his country needs.

What if Twilight Sparkle's letters to Princess Celestia started a religion?

This is the story of Brother White and Brother Scroll. One of them is an upstanding young unicorn eager to do whatever he can to make other ponies happy. The other is a shy little loner who's never had a real friend before. What do these two young stallions have in common? They are both members of the Fraternity of the Joyous Friends of Princess Celestia, an organization dedicated to teaching Equestria and the world about the magic of friendship. When Scroll and White are assigned to Earthquake Island, however, they find themselves in over their heads. Can the teachings of the Book of Friendship help them save an island run by a brutal warlord, wracked by war, poverty, and hatred?