Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

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.

Applejack finds a strange visitor in her apple orchard one day, with even stranger stories to tell...
MLP/L4D2 crossover. My first story on FiMfiction.net! May add more tags as story progresses.
Credit for the image goes to brokencreation on DeviantArt.

The star system Omega Centauri was just another oddity on a map to scientists in the not too distant future. However when they found the star was orbiting an earth-sized, earth-like planet instead of a black hole as its motion had suggested, a mission was scrambled to investigate this most unusual of celestial behaviors.

Hamstrung by politics, and nearly crippled before it began, the 'Lone Ranger' mission was reduced to just one crew member and left to his own devices.

These are the logs of Arrow 18 and its lone commander. This information is classified TOP SECRET by the Global Space Agency.

Do NOT tell the princess.

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*)

The Princesses find an alien creature barely clinging to life at the scene of a terrifying crash. Can the Combined Power of the Elements of Harmony save it, or more importantly, should they save it? Will the arrival of this strange creature tear Equestria apart?

TV Tropes
https://tvtropes.org/pmwiki/pmwiki.php/FanFic/Article2