Scootaloo has an adventure of rather big proportions!

This is a collection of updates for a forum adventure as told by Scootaloo, and is such formatted in a way much different from how fanfics are normally read, due to being set up for reader interaction.
http://www.mspaforums.com/showthread.php?40963

Memories of a time long gone by hold the key to Luna's salvation. To save her sister, Celestia sends Twilight on a quest through Luna's mind, searching for the source of an ancient spell that is slowly killing her. What she finds may change her forever.

Twilight experiences Luna's life first hand on an emotional journey through the dark alicorn's past.

Pinkie Pie is haunted by feelings of self-hatred, stemming from the day she left her family to be on her own. Never wanting to see her best friend in a crazed state of distress again, Rainbow Dash resolves to reconnect her with her estranged family and bring an end to the personal demons once and for all.

Featured at Equestria Daily on September 28, 2011.
Featured at Canterlot's Finest on November 21, 2013.

After her students release the spirit of Discord on an official field trip, Cheerilee finds herself out of a job. With no opportunities in Ponyville, the schoolmare takes a job offer in the inner city area of Canterlot's old mining town. Can even she overcome the insanities of her colleagues and apathy of her students in time to pass her next annual review? And who is the mysterious backwards-talking filly following Cheerilee around? Luna's School for Disadvantaged Youngsters will never be the same!

Tv Tropes page can be found here.
Cover art based on work by blackgryph0n, used with permissiom.

The Sequel to Number 12.
The Doctor and Twilight leap into the future, though it may be a far darker place than they envision. In the mean time somehow the Doctor keeps crashing around Ponyville, something to do with Fluttershy, but what?

Luna has had enough of Celestia's games, and has found the perfect means of revenge. Using a long-forbidden spell, she transforms her sister into little more than a small filly, all so she could pull the greatest prank ever. Unfortunately, she soon learns that before you fool around with dangerous magic, you really need to read the fine print...

A sequel can be found here.

Cancelled, but preserved for posterity.

Archer is not having a good day. He's recently been knocked unconscious and imprisoned by a Fae race, notorious for their animosity towards humans and each other. Instead of cannibalistic Merfolk or mischievous Fairies, he finds... talking ponies. Who want him to be their "friend."

He is sentenced to remain in a small town they call "Eqshana", until he can learn to "live in harmony" with its inhabitants. Unfortunately, a message from his king, Jove V, has turned his prison sentence into a mission of espionage. Now he must escape these no-doubt insidious creatures, and even more importantly, stay sane doing it. Along the way, he will answer one of the most important questions he has ever faced: Is there really nothing to eat around here besides hay?

After Nightmare Night, Luna invites Twilight to tea, and they start spending more time together. Princess Celestia teases Luna about it sometimes.

This is the story of the end. This is the story of the death of Equestria. It is the story of the reign of her royal majesty, Princess Twilight Sparkle of the Fading Sun.

The alicorn sisters are dead and Equestria has turned to Twilight Sparkle to guide it. However, just maintaining a dim sun a fraction as bright as her mentor's keeps the new princess near her limits.

Years have passed and Twilight Sparkle is sure of only one thing. Equestria is dying.

NOTE: Written before "It's about Time" in season 2. Everything after "Read it and Weep" was ignored throughout this story.

Robert Parker is a 24 year old ex-web developer living in New York city. In the wake of the conversion movement, he has seemingly lost everything. Haunted by the same nightmare every night, he soon realizes that he must make a choice.

To those unfamiliar with the Conversion Bureau: it is a scenario created by an author named blaze in which Ponies either appear in the human world or have lived beside humans without incident for millennia. One day, in the face of all the damage humanity has done to its world, the ponies offer a solution: undergo conversion to become a pony and allow the world to be inundated with Equestria's influence: thus healing it and bring forth a golden age.

Many different authors have taken many different approaches to this idea, all of them are worth checking out.

http://www.ponychan.net/chan/fic/res/53616.html (The current thread)
http://www.equestriadaily.com/2011/04/conversion-bureau-compilation.html (The compilation post on EQDaily. *NOT UPDATED*)