In the many years after the Conversion Bureaus' shutdown, Twilight Sparkle is tasked by the Princesses with finding the last living human on Earth, Isaac Hamilton, and learning the story of his past. What she hears is a tale of loss, tragedy, joy, and the discovery of one's place in the world. But how much longer would that place last with what Twilight has to tell him?

Twilight and her five friends are transported during a botched spell, across dimensions to... Ponyville, Equestria? But not the same one that they knew. Sitting on a bench is Harpsy and Babar. The Doctoress avoids apples from an aspiring Applebuck. And in a library across town, six stallions join their forces as they try to decipher the appearance of filly look-alikes of themselves around Ponyville!

Pinkie Pie is visited by a strange customer whilst working at Sugarcube Corner. Hilarity ensues.

When Rainbow Dash's newest trick backfires spectacularly, she and Fluttershy find themselves stranded in the middle of nowhere. Together, they'll have to survive and find their way back to Equestria and Ponyville...no matter how far the journey.

Now with a Spanish translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/Apoteosis-1-3-857109863

(Originally submitted to Equestria Daily)
Art by katwalk.

Metal Gear has fallen into the hooves of an Equestrian revolutionary, who, with the backing of his human mercenary allies, intends to use it to depose Celestia and crown himself ruler. Having crossed into Equestria in pursuit of this rogue weapon, the legendary Solid Snake must ally with the residents of Ponyville to prevent a nuclear catastrophe.

See also Equestria Gear Solid, the hilarious spin-off EQG parody in which everything you know is wrong, and every single character from the story is an awful caricature of themselves.

Now with its own TVtropes page!

The Ponyspawn have invaded Equestria, and it is up to the newest addition to the Grey Wardens, Twilight Sparkle, to find the means to drive them back! With her friends and allies at her side, can Twilight defeat the evil tide before all of Equestria is devoured?

The Sequel, Pony Age: Catalyst, is available.

In the 31st Century, humankind has spread to thousands of planets in the Inner Sphere. Once united under the glorious banner of the Star League, the Successor States and their noble houses now fight bitter wars over the scraps of empire. When a JumpShip carrying a special task force from the Federated Suns suffers a catastrophic misjump, the occupants find themselves stranded above a strange, beautiful world at once alien and eerily familiar.

Meanwhile, in the peaceful realm of Equestria, Ponyville’s resident bookworm , Twilight Sparkle, has stumbled upon hints of a secret buried for centuries. A secret that may lay bare long-forgotten aspects of Pony history and culture.

Our story begins on the planet Valexa, where the beleaguered Militia has launched a last-ditch effort to call for help against overwhelming odds.

Written with those who are not familiar with the BattleTech/MechWarrior universe in mind.

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

Luna discovers something hidden from Celestia for twenty years, now, with emotions running high, she enlists the help of the Mane 6... but what seemed to be a single mystery, soon reveals a darker and much more complicated plot that will soon decide the fate of Equestria.

Check out the Empty Room TV Tropes Page (Warning: Spoilers!)

Revised chapters edits and proofing (with many thanks) by: lammy, Trevor, Nick Nack, Fifth Alicorn