The story follows a Human turned pony in Equestria. He knows nothing of the MLP universe and must learn to adapt to this new life. The Wonderbolts are main characters in this.

Comments are appreciated!
Art by Swaetshrit (No longer drawing) commissioned by Derpytwizzle | Full Image

"A wise man once said: Don't rock the boat, let alone break the very fabric of realities, but I guess your pay grade allows you to do whatever you want, right Horowitz?"

"Listen Cooper, this is serious. I mean BIG, we're talking international involvement here! Regardless, I must ask: what do you know about Horses?"

"As much as any man, I guess"

"Well, break out your Stetson and boots, I need you to go somewhere for me."

When English teacher Connie Hayden is told by a mysterious new friend that there is a way to travel from the human world to Equestria, she doesn't believe her. But what if the legend of Pinkamena is true?

Illustration by the talented BambooDog.

Cyrus, a young man, living on the western seaboard of the united states is one day handed a vial of liquid of unknown effect and origin by a drug-dealer snooping about his neighborhood. He learns to live with hooves, a tail, a mane, and as a MARE. He deals with the social stigma of being a pony pre-conversion bureau opening and lives with the fact a decent majority of his neighbors are HLF members.

A tragic accident robs Jay and many of his friends of their parents. Seeing no alternative aside from a life on the streets and poverty, they enroll in the Conversion Bureau program to emmigrate to Equestria. When Jay finds out that his close childhood friend and crush, Chloe, is going as well, he takes it upon himself to win her affection before the end of their ten day stay.

It's not real, it can't be real. Ponies are just cartoons and some fanfics on the internet. The wings, the hooves... I'm just having a bad dream!
I wish that were true. But pain, friends, and a strange drink are telling me this is all too real. I'm a pony now and I think the world is falling apart.
People, the end is nigh, the world has decided to go out with a bang, and it's taking us along for the ride.

*Loosely based on "The Conversion Bureau" universe.*
*Note about the art. Chatoyance was very kind to create some fan art. Just as a little note though "John" has brown hair not bond. Just a little tidbit to keep in mind while reading. Thanks so much again Chatoyance!*

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

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*)