More specifically, it was an oak tree. And its name was Forrest. Did I mention that Fluttershy meets it? Well, she does.

Not to be taken seriously, might I add.

On a way home from a party a mare ends up unconscious. When she comes to, she is subjected to a secret version of history from a mysterious alicorn, one which will change her view and her life forever.

Twilight Sparkle has been captured to the Lazarus tower, an ancient research facility located in the center of an remote island.
Built by Nightmare Moon over a thousand years ago the tower was created to research resurrection using dark magic.

Now it falls to the hooves of Rainbow Dash and Applejack to travel across the island ravaged by dark magic and enter the tower in secrecy to save Twilight all the while avoiding the gaze of a mysterious villain who has taken control over the island.

Sam wakes up in Equestria stark naked and with no clue how he got there. More problematically, he seems to be in somepony's home.

Teen for nudity and the awkward situations arising from said nudity.

A rewrite of Make Friends, or Die! by Sam Polson (which has since been taken down). I liked the premise, but Sam's English was spotty and Google Translate didn't help him much. Starts going in its own direction fairly quickly.

"Pale" is a story following the main character, Pale, hence the title. Pale is a mare with more than a few strange things about her. She lacks a cutie mark even though she has reached adulthood already, and she lacks the ability to show emotions. Her mane and coat are both brighter, happier colours, so many are mislead by her appearance. Her parents are both extremely successful scientists; Doctor Engram being her father, and Doctor Cerebellum being her mother. Both her parents are unicorns, and throughout her family tree, her ancestors are all unicorns as well, but Pale, herself, is neither pegasus or unicorn. She is an earth pony, it seems, but with her strange life, she very well could be something else. The plot focuses on Pale's mysterious and rather confusing history catching up to her, including the death of her mother and many other hardships similar. Through many twists, turns, accusations, and misunderstandings, Pale ends up being chased down by the forces of good, including the Mane 6 ponies with The Elements of Harmony ready to strike.

After the incident a the Royal Wedding in attempting to steal the love of Shining Armour from her sister, Cadence, Queen Chrysalis is left banished to the Crystal Cave. As she stares to her reflection in the walls of gems, she recalls the memories that turned her into a dark being. As she delves into her past of pain, misery, and heartbreak, she discovers that maybe anypony can change... Or can they?

Justin gets sent to Equestria through a Portal gun that Luna made for the Mane 6. Unfortunately, after Justin was transported to Equestria, the Portal gun was broken by Rainbow Dash. Now he is trapped in Equestria, with no way returning home. How will things turn out?

When the Changeling Commander wakes up, he finds himself on a quest for his lost swarm.

But what happens when you get caught yourself? Well the answer to that is that you are pretty much doomed at that point.

Follow this heroic (foolish) changeling as he embarks (stays in a cell all day) on a magnificent (dull) quest to find (plays tricks upon) his lost battalion!

(Image by ~Iaomai)

For killing thousands, after the Earth's military experiments messed him up, he got sent into space, hoping that he will never come back. He found home on a desert planetary system, and after living alone for over one thousand years (thanks to the military), he recovered his mind, then got caught by a anomally and transported into Equestria. Will he find peace, or he will make war? Will he return? Noone knows.

I woke up in my cell again, the magic barrier prevents me from experiencing anything beyond the confines of my cell. My only contact with the outside world is the occasional visit from the doctor. I'm not crazy, not mad or insane, I'm just a test subject. My name is subject 7, the tests done on me are excruciating and almost kill me, but something deep inside me burns. A fire that tells me to live on for one day I will be free.....and that day came sooner then I thought.