The Elements of Harmony are defeated and Nightmare Moon stands on Equestria's throne as their new Queen. Is Equestria doomed to suffer through night time eternal or will they be... perfectly fine? Twilight finds her new job as slave or "personal assistant" to her new ruler to be a bit maddening. But is this evil sarcastic queen really as bad as she originally believed? And just how many others are diabolical enough to cash in on the change in staff? Can Nightmare truly run a peaceful Equestria? Let me just answer all these questions right here in the description...

A dark secret lives in the kingdom of Canterlot and for thousands of years a select few have guarded her. Yet what hope do mere ponies have of maintaining the delusions of a god?

Apple Bloom doesn't know what her special talent is. But after an incident in the Everfree forest, she starts to have some dark suspicions about it. Her choices will echo through the ages, and they will call her Warmare.

Inspired by the popular Modern Warmare fanart.

After a mysterious Unicorn named Venser falls from the sky, ponies start acting strangely all over Equestria. As the problem spreads, Venser has to band together with a small group of ponies who remain unaffected to fight off an invading force that's already won.

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*)

An excerpt from an incomplete fanfic expanded into a series of shorts.

The rule of Discord may be over, but it left behind an unexpected legacy. Ponyville is no stranger to crazy ponies, but how will it cope with a being born from pure chaos?

Twilight and Spike are sent a message from Princess Celestia, stating that a dragon will be staying in Ponyville. Spike has to go into hiding, Twilight has to organize the arrival and the others have to cope with the usual insanity. Oh... and the crusaders are doing their thing. Do I smell doom?

Not even a week has passed since Discord's defeat and Equestria's future is once again at stake. Will Twilight be able to learn the cause of tragedy in time, or will evil reign supreme once more?