This story is a sequel to The Rainbow's Surprise

On the day of Fluttershy and Rainbow Dash's wedding, Princess Celestia left Twilight a message saying that she should prepare herself if something happens. The next morning, Twilight awakens to find that all of Ponyville has succumb to a blinding fog. She must now travel a monster-filled town in search for her teacher and friends and try to return Ponyville back to the way it was.

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

The story follows the events of the most devastating war in Equestrian history, and four of the many lives that are changed by it...
Rivet, a timid young griffon, leaves Cloudsdale in an attempt at a fresh start, and decides on Ponyville as the best place to find it. But he has barely settled into his new life when the entire nation is plunged into war.
Big Macintosh, a 'gentle giant', struggles with his own identity as the war slowly strips away everything that made him who he is.
Shining Armor, a prince of Canterlot, joins the struggle against the invaders, intent on doing everything he can for his people.
Zeniah, a naive young zebra, cast into the flames of war out of desperation.
But the fog of war blurs the line between friend and foe and, as the war progresses, a deeper conspiracy is slowly revealed...

After being abandoned by her mother in the Everfree forest, Derpy is taken in by the kind earth pony Mary Doo, who tries to do all in her power to unlock Derpy's inner genius from her seemly broken body and mind. As Derpy learns to communicate she also learns the secrets of the world, makes friends, falls in loves, all on her quest to learn to fly so that she may finally accomplish her life long dream and face her face dark past.

This is a spin-off of Bubbles: http://www.equestriadaily.com/2011/03/story-bubbles.html

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

Octavia Philharmonica is a desperate mare. Her involvement in the ill-fated "pony pokey" at the prestigious Grand Galloping Gala has left her blacklisted among the elite of Canterlot who form her clientele. Faced with the possibility of being evicted from her apartment for inability to pay rent she decides to take a temporary job at a local nightclub. Of course, she's never set hoof in a club before and has no idea what she's getting involved in . . .

A single changeling is blamed for making Chrysalis' plan to take over Equestria fail. He's banished and thrown out of the hive, ending up somewhere far away.

Luckily, he ends up not too far from a certain well-known village, where he can feed to his heart's content.

Needless to say, not everything goes according to plan.

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Now with a French version, courtesy of Wansdich, here.
Fanart! Check it out here. And even more here!
Now in ereader-friendly PDF version, by Starflower Hooves! You can view and download it here.
Featured on Equestria Daily!

Princess Celestia tires of constantly being surrounded by decorum, deference, and formality, and decides to take a day off from being Princess. But visiting Ponyville incognito is harder than she expects. Will she be able to fit in and make friends without blowing her cover?

Luna's finally ready to get back out there into the world of Equestria, ready to see what's become of ponykind in the past thousand years. Except... she's not quite ready to go out on her own, amongst ponies that know only tales of nightmares and betrayal about her, and the one pony she knows personally is a little busy running a kingdom and raising the sun. When the offer for companionship comes from an unlikely place, Luna learns two great lessons. One, the risk to get to know a pony can lead to great rewards. Two, socks make everything better.

When Applejack goes with Rainbow Dash on a trip to Fillydelphia, she learns that life doesn't always go according to plan... and that can lead to something better. Written because I wanted to do my take on a shipfic, minus what always annoyed me.