The sequel to An American Dude in Equestria

Years after returning to Earth, the human finds himself once again brought to the ponies' world. This time, however, his friends don't recognize him and their adventures are dictated and observed by Discord himself. Deception, pain, absurdity, and tension abound.

You're a letter-sorting unicorn who works at the same post office as Ditzy Doo. Sure, you're both good buddies, but a small part of you wonders if you could be something more. One day, Ditzy gives you a gift...

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

Colonel Robert Gordman finds himself trapped in the land of Equestria after being mysteriously transported from his home in Dayton Ohio to the Froggy Bottom bog. Loneliness and Starvation over come him, until he discovers the bizzare inhabitants of this new land. He has a son back on earth and his wife is expecting another kid, Robert cannot afford to stay here any longer. He must find a way to return home, even if it means kidnapping ponies in order to gain the attention of Celestia.

During a brilliant meteor shower, an unknown object lands in the Everfree Forest, carrying one sole occupant, a creature nopony has ever seen before. What is its purpose here? Does it seek peace, or destruction?

Update: Sorry guys but I am having an incredibly difficult time deciding where to go with this story. Putting it on hiatus until I can decide where I want to go with it.

All rights go to hasbro, Lauren Faust, yada, yada, yada.

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*)