It is the thousandth year since Nightmare Moon's banishment and she has returned. When the battle with Nightmare Moon goes awry, Twilight's friends and family must cope with the destruction left in Nightmare's wake.

Note: This story is based off of the picture giuliabeck's You Are Mine and Sparkle No More.

Distance can drive us apart. It can also bring us closer together.

After all is said and done, and the ponies have gone their separate ways, the only way they have to keep in touch is through letters.

Original Equestria Daily post is here
Russian translation
Chinese translation
Polish translation
Spanish translation

Now with music and audiobook

It's strange how a short few years can seem like such a long time ago, Twilight remembers the moment she was told the truth about her, and how she would outlive all her friends.

Shining Armor and Cadence's spell reveals something completely unexpected as it expels Chrysalis and her changelings out of Canterlot: A secret kept from everypony for several years...

Now with a TV Tropes page! Warning: Will Contain spoilers.

Sometimes, bad things happen to good ponies. A year following a tragic incident, Twilight Sparkle returns to Ponyville to visit what she has been missing - her town, her memories, and most importantly, her friends. But will everything be as she remembers it?

This story has a sequel titled "In History, Maybe".

A story in the same vein as My Little Dashie, but not a carbon copy.
Awoken in the middle of the night by a mythical creature sitting on his doorstep, a man's life is drastically re-arranged by the sudden entrance of Princess Celestia. Struggling to accept things he couldn't ever think possible, he'll have to make a decision about what's worth changing his entire life.
(Note: I added the "Alternate Universe" tag because I imagined this being a reversed-roles universe where Luna is the big sister and banishes Celestia, rather than the other way around.)

Everything has its origin. Who is Celestia's mother? All secrets have an end. The Fausticon, Lauren Faust, has dreamt of the day she would re-unite with her five children - Cadence, Celestia, Discord, Chysallis, Luna and Nightmare Moon. But...it remains unknown to her what her children had turned out to be since her departure...

MLP:FIM/Avengers crossover

Loki has received his punishment, one he hadn't even thought of. Now he has to live in Fluttershy's cottage, as a cat, while trying to get his magic powers back. But even a regular cat can create Chaos if he wants it bad enough.

Or perhaps he'll learn new kind of magic: The Magic of Friendship.

Scootaloo has always had a mysterious past, but when she reveals her secrets the her friends, will her friends still accept her, especially after learning she was never even a pony in the first place. With secrets revealed, and new enemies being found everywhere, only time will tell the fate of the Cutie Mark Crusaders.