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*)

This is a direct side-story spinoff to "A Twist in the Tail".

Edge used to be human. She used to be a man. Then one day, she was foolish enough to break into a Conversion Bureau to steal some Potion. Believing it all to be a plot to 'scoop out the brains of humans', he downs it. She wakes up as a pegasus pony with an audience with the princesses...

For her crimes, she is sentenced to community service.

This won't end well ;)

After the disastrous invasion of Canterlot, an injured changeling wakes up near a small cottage and is quickly discovered by two of the last ponies she ever wanted to see. Now, with the help of her new "friends," she has to remain undetected in a town high on changeling hysteria that would not hesitate to throw her in the Canterlot dungeons should her true nature be revealed.

Simple, right?

Too bad she couldn't have picked a worse form to stay inconspicuous...

Many thanks to ZuTheSkunk for the cover image!

Have you ever had a dream that just seemed so real, that it was impossible to say for certain that it was even a dream at all? A dream that, despite all of its impossibilities, seemed to re-write your entire perception of reality, re-writing your sense of what—and indeed, who—you are? Accepting change is hard enough as it is. But when you're a somebody who wakes up as a somepony, how do you cope with the impact such a drastic change has on your mind and body? With changes like these, it must surely just be a lucid dream—albeit a suspiciously accurate one—just brimming with potential and ripe for exploration. So you might as well suck it up and make the most of these distressingly…unusual circumstances, and seize this psychological adventure before you wake up and the dream ends.
After all, this couldn't possibly be real, so the dream must come to an end eventually…right?

This collection of stories is set in an alternative Conversion Bureau timeline where Mankind reigns triumphant, having destroyed Equestria and sent it back into the sea. The only remnants are Celestia's severed head and the now-docile earth ponies that are made from her blood.

As mankind claws itself back from the brink of extinction, it must build a new society and move forwards into the future, with a changed destiny shared now by two sentient life-forms. In this collection, stories will be spun about sacrifice, loss, and nobility of spirit, of two hands and four hooves.

new title card from http://mi9.com/shattered-horizon-intro_77122.html

Los Pegasus is the new name of what was once Los Angeles. The Equestrian barrier, now on land, approaches, and with it Inclusion Day, where the city will become part of Equestria. Both converted Newfoals and the last humans all have their own stories to tell as this final event in the life of their city approaches.

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 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

"My name is Lyra Heartstrings, and you will not remember me. You won't even remember this conversation. Just like with everypony else I've ever met, everything I do or say will be forgotten. Every letter I've written will appear blank; every piece of evidence I've left behind will end up missing. I'm stuck here in Ponyville because of the same curse that has made me so forgettable. Still, that doesn't stop me from doing the one thing that I love: making music. If my melodies find their way into your heart, then there is still hope for me. If I can't prove that I exist, I can at least prove that my love for each and every one of you exists. Please, listen to my story, my symphony, for it is me."

Cover pic by Spotlight: askspotlight.tumblr.com