Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

After a mysterious and widespread spell causes ponykind to vanish, Fluttershy is left behind to cope with what the future has in store for her and the remains of Equestria.

In a matter of days, the once-prosperous nation begins to descend into a harsh and unforgiving place. While cities crumble around her, Fluttershy finds herself living in a land rife with dangers and heartbreaking reminders. With nopony to turn to, Fluttershy is forced to learn to fend for herself, discover what happened, and, if possible, find a way to reverse it.

Survivor Shy is an illustrated story following Fluttershy in the weeks after a magical cataclysm. While the last pony relives her past, readers are offered a vivid glimpse into Fluttershy's mind and are led on a harrowing journey through the ruins of Equestria and beyond.

Story branches out before Season 3 Finale.

In-progress Reading by Finish Line available
In-progress Russian translation by Papilion_star available.

After an accident, Rarity and Twilight are thrown in a race against time to stop their transformation into changelings before they become part of Chrysalis' swarm forever.

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

Twilight wakes up and finds out that she's changed back into a filly! What kind of trouble will she get into? How will her friends react?

Some accidents are small, and some endow you with the power of a godly ruler. On the opposite end of things, you lose your wings along with your ability to move celestial bodies, and you can't tell anypony. Why, because what would they think if the princess became a librarian? It's going to be "fine". Celestia just needs to switch back with Twilight before either of their true identities are revealed. All Twilight has to do is hold down the castle, fight off scheming villains, run the country, and worst of all... deal with all the noble ponies.

Rated teen for shenanigans and some more serious parts. Takes place at the end of lesson zero. Please tear this apart with comments. I like criticism. Comment if you have issues, don't leave me with a mystery thumbs down.

This story is a sequel to Princess Celestia Hates Tea

Princess Celestia helps to banish a hoofful of inner demons lurking deep in the heart of a troubled author. Metafiction, again, ensues. Something of a coda to "Princess Celestia Hates Tea".

Now with a Spanish translation by Spaniard Kiwi!

Now has a sequel! Celestia Does Stuff in Ponyville While Other Things Happen Elsewhere

"Your Majesty!" "Your highness!" "My princess!" "My Sweet Goddess!"

These are all titles that Celestia has heard her little ponies call her. They hold her in the highest esteem, praising her for every little complement she gives them, and they look for her approval above all else.
Even her student Twilight treats her very highly, although that could be chalked up to a mother/daughter relationship. In fact, the only ones that don't treat her as a high and mighty, so-far-above-from-the-world-you-would-not-understand ruler were those not under her, and her sister.

Yes, everypony worships the very ground she treads upon.
And she is sick and tired of it.

With the help of her dear sister, Twilight and her friends, our beloved princess will seek out a way to put an end to the high level of praise that she has, Luna is jealous of, and Twilight is worried about receiving because of her status-- no matter how humble her subjects are to her.

The picture here seemed to get the premise of the story right. yes, sue me, I picked a picture to fit with the story, not a story for the picture. Please give the artist your full appreciation!

If you want to read the old and rejected chapters, consult this link [Clickey!]

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

Cheer up, Twilight. It's not every day somepony changes species. In fact, no pony has ever changed species. It's something new and you like discovering new things. Granted, Equestrians don't like new things, especially things that fundamentally alter their government. So maybe there is reason not to be happy after all.