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.

Rainbow Dash and Fluttershy have always been best friends, doing everything together. After a sleepover with friends though, a simple dare leaves the two in a complicated situation with mixed feelings emerging and bizarre misunderstandings ensuing.

Co-written by Souldin and Rated Ponystar

Prince Blueblood thought the Grand Galloping Gala was over. He thought he could just go to sleep and put it behind him. He never expected to be reliving the same disaster of a day, over and over... and over.

TV tropes page here:
http://tvtropes.org/pmwiki/pmwiki.php/FanFic/TheBestNightEver

Thanks to all the people who wrote the page and all the people who gave me a little wakeup call and comment to become aware of that fact! You can't see it, but you guys put a real smile on my face tonight.

Also, recently, extra thanks to RD Dash for giving TBNE a thorough editing. I've updated the fic accordingly (7.11.12)

Princess Luna, carrying out her normal duties of watching over the dreams of her subjects, comes across one of a more intimate variety. Normally unfazed by such dreams, this one embarrasses her into leaving quickly. Despite her decision to never think about the dream again—like always—she can't help but remember a single detail from it. A detail so strange she feels the need to talk to the dreamer about it. Unfortunately, she doesn't know who the dreamer was.

Awkwardness ensues.

For more story, read: One Day in the Life of Princess Celestia
For more awkward comedy (and story), read: Everypony Knows About the Wet Dream

After a mishap involving the Transportalponder, the Courier finds himself in a place he doesn't recognize. With no way back and nothing else to do, he decides that wandering into the nearest town is the best option. Being the Courier, things aren't that simple...

A Fallout: New Vegas/My Little Pony: Friendship is Magic crossover

The style alternates between omnipresent third-person and the Courier recounting his tale to... Well, take a guess.

Luna has been banished to the moon by her sister. After 1000 years in isolation, the poor alicorn is truly sorry for what she did and is ready to come home. But when a strange visitor befriends Luna in her isolation, the two find their stories of banishment to the moon merit many similarities. Luna's new friend offers her the key to her escape, but also rekindles the hatred in her heart, a hatred that took the mare 1000 years to forget.

Also, cover art not by me! I'm working on drawing ponies, but not a great artist. Cover art by HeriticOfDune

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.

Twilight Sparkle finds a book in the library.

Twilight Sparkle reads aforementioned book.

Twilight Sparkle's life is thrown upside down, her view of her teacher shattered, and her friends pitted against each other.

Everything will return to normal.

One of these statements is false.

There was only one explanation. For all of it. All of the strange, erratic behavior. Her irrational fear of the sun. Her nocturnal habits of locking herself in in the dark and closing all the blinds. Wearing her sunglasses everywhere, even inside! It was time to invest in some silver, garlic, and a wooden stake.

Luna shoves a cellphone up her plot, and the result is GREAT, CLASSIC LITERATURE!
Also a fart joke.
I'm very sorry.
Written in 30 minutes while singing (no, not listening to, but literally screaming it at the top of my lungs) Psychostick's "Dumb Song."
Image stolen from this sane individual.