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

Chrysalis kidnapped a dozen ponies, threatened Equestria, was betrayed by her own kind, and has now vowed vengeance on Starlight Glimmer before leaping from the ruins of her castle and flying off. She is definitely going to get away.

Absolutely.

Yep.

Reading by TheCaptainSand - Scarlett Blade

Translated into Spanish by ZodiacalComet

After saving Camp Everfree, Sunset Shimmer just wants to kick and celebrate like any typical teenaged girl. Or at least as typical as one can be when you now possess magic powers that let you see into the hearts and minds of others.

But memories are a fickle thing, and when Sunset Shimmer runs into her ex-boyfriend, she soon discovers that even a memory can be deceptive.

Special thanks to SolidFire for his editing work.
Cover art by Ponut Joe (can't link cause super-NSFW tumblr)

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.

When trying to focus on her studies, Sunset Shimmer is stuck watching an annoying little filly who just won't let her study.

Original Art by Baekgup

Cover image by Novel-Idea

Now with Reading by Wubcake

It had seemed like a good idea at the time, until Sunset actually read what Twilight wrote in her letter. She'd already said yes to seeing Celestia again, and she wouldn't go back on her word. As long as she remained convinced that this was a good idea and that it would all end well, she could get through it without a problem.

6/21/2016: Now with cover art designed by the very generous Novel-Idea! Thank you so much!

One beautiful morning, Twilight Sparkle decides she wants a free salad. After a small amount of theft, assault, battery, and arson, she sits down to enjoy what is sure to be the best tasting salad ever.

...Or she would have, if it weren’t for the Equestrian Intelligence Service locking her up as a potential threat to national security. Now, Twilight must escape a maximum security holding facility hidden deep underneath Canterlot. And to do it, she’ll need a paperclip, a spymare catsuit, an escape plan, and an alliance with the dastardly Drakbog, King of Frogs.

While strolling around town, Twilight Sparkle accidentally knocks out Derpy's contact lenses, revealing perfectly normal eyes hidden underneath.

So what else could Derpy be faking?

After the birth of Princess Cadance's fourth child, an adorable little pegasus filly, Princess Flurry Heart wants to know why none of her brothers and sisters are alicorns.

Her parents claim not to know why she's different.

They're lying.

There is now a Spanish translation of this story, courtesy of Spaniard Kiwi

An accident reveals a secret that nopony ever knew....

Inspired by this picture.
[img]http://i14.photobucket.com/albums/a331/brittmcgee/MLP%20Minecraft/TLSOA_zps2aa17c49.png[/img]