There is a very good reason that Princess Celestia sends Twilight and her friends to do her dirty work.

There is a very good reason that immortal, impossibly strong alicorns have a fleet of guards.

The newest Princess of Equestria needs to learn what strength really means to an alicorn.

Through unknown means, Sombra amassed an army and launched an attack against the Crystal Empire and a changeling sub-hive. This forces Celestia and Chrysalis to meet, and agree to a temporary alliance between their kinds. Neither is happy about the situation, but for the lives of the ponies and changelings they lead, they are willing to do what is necessary.

Yet, as weeks and months pass, the pair find working together is not as horrible as they originally believed. Is a lasting peace, and perhaps more, possible between ponies and changelings, between a princess and a queen?

Written for Equestria Daily's Super Happy Hearts and Hooves Lovefest Fanfic Event

Vanilla Torte lives an unassuming life outside of Canterlot, never thinking much about the huge city above.

Then something lands with a thunderous crash in his garden.

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

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

In a world full of magic, mere words can pose a deadly threat. When simply reading a sign can instantly infect the unwary, and cases start to turn up all around Ponyville, Twilight Sparkle casts the only spell she can find that can give her the time she needs to find the cause of the plague. But then she has to figure out how to stop the epidemic... without being able to read.

Editing provided by Spabble
If you like this, try Rainbow Typhoon
Audiobook on YouTube and for download on SoundCloud
Spanish version translated by MIkimoco
Russian version

When Twilight went back home, she left Sunset Shimmer to the care of her friends. Thirty moons later, she returns to Equestria, seeking judgment for her crimes from her former mentor, hoping that some form of punishment - a stint in the royal dungeons, perhaps - will help her come to terms with the past. If only it were that easy.

Can a rift like the one that has grown between Sunset Shimmer and Princess Celestia even be closed at all?

A story of past mistakes, resentment, the possibility of forgiveness, and hope.

A rather terrific dramatic reading of this story performed by Goombasa is available here!

Centuries after most of her friends have all passed away, Twilight decides to make one last trip into the past. No interacting, no greeting deceased friends, no reunion with her beloved marefriend. Just one quick glance at a life long lost.

However, for better or worse, she'll end up getting much, much more than that.

This story has a prequel entitled The Last Train Home.
Cover art by Swan Song

Princess Celestia has been keeping a dark secret from her subjects for a very long time.

It's not an easy truth to tell, but if anyone can accept her after learning it, it will surely be her most faithful student.

Third Place Finisher in Equestria Daily's 2013 Nightmare Night Contest!

Inspired by her favourite books, and keen to settle once and for all who's the fastest, bravest, overall best pony around here, Rainbow Dash challenges Applejack to a race full of perils and pitfalls. To the winner, the title of Most Awesome Pony. To the loser, defeat, shame and ignominity. But when the dangers start getting a little too real, they have to decide what's more important. Victory, or friendship.