In Equestria, humans serve the ruling pony class. Their lack of magic makes it near impossible to survive on their own, and so they depend on their rulers to protect and help them, and put a roof over their heads. But on Earth, and in many other solar systems, their strength is the pinnacle of hope, as they assist those they can in their frantic search for the ones who came before.

Near the edge of the humans' empire, The USSF Monarch stumbles upon Pony kind on Tango 126, one of the many targets during their hunt for the Precursors. Their curiosity is peaked, and John Punch, a high ranking Elite, is sent in disguised as one of the many Human occupants on the planet, to learn of their culture, and the Precursors' presence on this planet.

Now the respected veteran must face the social challenges of being thrust into a gender reversed, pony dominated society.

In Equestria's far future, one thousand and five years after the return, a dysfunctional group of argumentative ponies must quest to defeat the most dangerous enemy of Equestria to ever live; the malevolent Lord Second, one of the only known members of the race of elder gods known as the humans, and the ancient cult who worships him, the Brotherhood of Man.

An over-the-top surrealist comedy, with slight serious elements. Expect a steady decline into insanity.

Cancelled, due to reasons of severe cranial trauma

Now with audio reading and prequel story, Shades of Grey, by Draven Eclipse.

This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

Subject Six is just another earth pony, conditioned for apathy and trained as a slave. But when humanity begins destroying itself the ponies need a leader, one to unify the desolate, the hopeless, the ponies. But can a species designed in a lab, and conditioned for slavery, truely grasp what independance is? And if so, can somepony unite them, and take advantage of humanities weakened state to overthrow their masters, creators, and enslavers?
As this is my first FanFic i'd appreciate any feedback you guys can give, no doubt many of you have written FanFics yourselves, complete ones at that, so you already know more than me :)

NOTE: There may be spoilers in the comments. Read them at your own risk!

A mysterious viral outbreak grips Equestria, threatening the very life of the country. In an effort to stop the infection, Princess Celestia orders all individual settlements within Equestria to be quarantined. Can Twilight Sparkle, along with the other Elements of Harmony, figure out the cause of this horrific virus and put a stop to it? More importantly - can they survive?

Rated M for Violence, Adult Content and Language.

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.

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey

A look into the felt and streamers mind of a pink pony who loves parties.

After her students release the spirit of Discord on an official field trip, Cheerilee finds herself out of a job. With no opportunities in Ponyville, the schoolmare takes a job offer in the inner city area of Canterlot's old mining town. Can even she overcome the insanities of her colleagues and apathy of her students in time to pass her next annual review? And who is the mysterious backwards-talking filly following Cheerilee around? Luna's School for Disadvantaged Youngsters will never be the same!

Tv Tropes page can be found here.
Cover art based on work by blackgryph0n, used with permissiom.

Twilight Sparkle believes she has perfected a process to allow Earth Ponies and Pegasi to teleport. Unfortunately, in the Land of Ooo, a bubblgum-haired princess is about to run a similar experiment. Will even all of the friendship in Equestria be enough to settle Finn down? Will Pinkie Pie ever get her doughnut? Perhaps along the way, everyone will learn that truly, friendship is ALGEBRAIC!