TVTropes page yay!A human arrives with a house in Ponyville. The Mane Six, and Princess Luna must deal with this new arrival. But not everyone agrees how it should be handled, not everyone agrees on what danger it represents, or the benefit it can be to Equestria.

The inhabitant must also deal with the new rules and conventions of this new world it knows nothing about, as well as the mystery of its appearance, and the incongruities of its arrival.
TVTropes page yay!

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

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.

One day on a trip to the market, Fluttershy discovers that things are getting caught in her tail. What kinds of things? Interesting things. Strange things. Their origins are all questionable at best.

Spanish Translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/La-cola-de-Fluttershy-1000352121

This story is a sequel to Justice

Worker's dreams have taken a turn for the worse. Feeling trapped, unable to talk about his experiences and unable to stop the near-nightly terrors, he wonders if he should reach out to the Princesses. It never occurs to him that these nightmares might be something more.
This is the final story of a trilogy. The first part is Order from Chaos, and the second is called Justice.

After discovering that Cadence is not who she appears to be, Twilight is sent to another world entirely by the disguised Changeling Queen to avoid her plan being disrupted.
When Twilight lands, she discovers that not only have Spike, Owlowiscious and Peewee followed her, but that they've arrived in a world where the main sentient species is human.
There's still a place where they teach magic, though.
Crossover with Harry Potter. Twilight will be effectively taking the role of Hermione.

I've marked this story as cancelled to reflect the unlikelihood of it continuing. If I do come back to it I'll revert that.

Twilight Sparkle is interrupted from a midnight study session by the arrival of three confused magic students.

A short Harry Potter/My Little Pony crossover. Can the universe handle Twilight Sparkle and Hermione Granger in the same room?

EDIT: Rewritten per 2015-04-27

OHMYGOSH OHMYGOSH OHMYGOSH by Scribble Worthswords

Shortly after the start of her maiden voyage the Equestrian Deep Space Explorer Red Shetland, commanded by Twilight Sparkle and Princess Luna, disappeared after reporting a reactor problem.

Three million years later, following her release from a stasis pod, Luna wanders the deserted corridors of the ship and tries to understand what went wrong. Along with the Ship's AI, a creature that evolved from the ship's cat, a hyperactive service robot and the resurrected holographic personality of Prince Blueblood, Luna must stave off boredom, keep the ship in order and find a way to return home.

Assuming she even has a home left to return to.

But first, she needs a drink.

Twilight Sparkle flagrantly abuses her Come-To-Life spell, and learns a little bit about love in the process. Also, puns.

Now with actual cover art, thanks to the generous SuddenlyFerrets!

Now with a Spanish translation by Spaniard Kiwi!

Derpy Hooves is secretly a changeling.

Nopony particularly notices, or cares.

(New 9/15/19: Spanish translation by Spaniard Kiwi! Thank you!)