First of the Savage Skies series.
After running afoul of timberwolves in the Everfree Forest, Fluttershy is saved by a mysterious young colt with a most unusual and disturbing feature. Realizing that he is alone, without anyone else to care for him, Fluttershy realizes that she must try to bring this lonely foal out of the forest and give him a life of love and friendship. The problem is that this colt's...unique qualities have made him more than a few enemies, including some who are closer to home than Fluttershy realizes.

Now with a sequel: The Promise of a New Day.
Now with a TV Tropes page.

"Hey, hot shot! You know me, right? Of course you do! Who doesn't know of the amazing Eddy? So, anyways...I had this great scam all figured out, right? It was the best scam ever, I tell ya! But then something went wrong - probably monobrow's fault, as usual - and now we're stuck in this weirdo land with these even weirder talking rainbow-coloured horses. Great. Still, I guess it's not all bad. New people - or ponies, whatever - means new suckers to fleece, and more money for me! Hey, don't look at me like that! I'm just looking out for my friends, that's all - who says I can't make a little money on the side, eh? Besides, sockhead will probably figure out a way to get us home in no time! What's the worst that could happen before then, huh?"

(Crossover with Ed, Edd 'n' Eddy. In the canon of this story, the events of Season 3 of My Little Pony: Friendship is Magic have never happened. The events of Ed, Edd 'n' Eddy's Big Picture Show have never happened, either.)

This isn't entirely my work. This story was started by kiddi. He wrote the first 4 chapters. He feels he can't continue and has given me permission to continue it.
Naruto Uzumaki is lost to Konoha when he vanishes durring an attack on his life. He winds up in the magical land of Equestria in under the care of a certain Zebra. But this is only the beggining as much larger things are in story for are young traveler. Watch as he grows and faces numerous challenges caused by his past and his future.

A routine space patrol leads the man of steel to a peaceful planet where ponies are the dominant species. At first, the ponies seem fine with some one like him helping out and protecting the ponies. But as they learn more and more about his power, the more some begin to fear him. For what do you do against one who is like a god? Will you learn from him and become stronger? Or fear him and do everything in your power to bring him to your level?

Not based on a particular Superman, but will have elements from the cartoon and comics, with his most known strength's and weaknesses.

I OWN NOTHING! Please comment and critique.

Before Twilight Sparkle found her friends and home in Ponyville, one of the few ponies she came to know was the Court Poet of Canterlot. And they were definitely, certainly, really, seriously not friends. At all.

Luna, Princess of the Night, feels like she's under quarantine in Canterlot. Apart from Celestia and her personal aid, Scrivener Blooms, Luna is treated like Nightmare Moon by the residents of the castle. After a journey to Ponyville, however, Luna takes an interest in attempting to make friends and begins to yearn to see more of the world and to prove that she is back in control of herself and regaining her old strength.

A mix of romance, high fantasy, and magic, the story features the power of friendship, sarcastic wit, and adventure against darkness driven by Luna's brash, courageous spirit.

The first story of the Nátta Edda, and beginning of the Fimbulvetr Trilogy.

While pursuing a splinter of Hive Fleet Behemoth, Captain Sicarius and the Ultramarines 2nd company are caught in a warp storm that carries them and their prey to an unknown planet. Meanwhile, Princess Luna notices something strange in space that could spell danger for all of Equestria. Swept up in a war between the terrifying Tyranid swarm and the vengeful Ultramarines, the ponies must fight for their lives in a war that spans a galaxy.

Thanks to thirdstring_overlord and GiftedMonster for proofreading my newer chapters. thirdstring_overlord also writes an excellent 40k crossover that needs some fans. Go check it out!

Disclaimer: I do not own My Little Pony: Friendship is Magic and Warhammer 40k. They are the properties of their respective owners.

In the dark depths of Asgard, Loki Odinson sits, punished for his crimes on Midgard.

But new developments cause the wayward son of Odin to escape his prison and seek refuge across the Nine Realms in a land very much unlike any he has ever seen: Equestria.

While Loki makes a new life for himself in Equestria, Thor must once again gather together the Avengers and give chase to his escaped kin. But will the lies Loki feeds his newfound friends send the Elements of Harmony on a collision course with the protectors of Earth?

(Cover image by the wonderful Reiduran)

The Death Korps of Krieg, seeking atonement from their government's betrayal decades ago, they give their lives willingly in the everlasting fight against the enemies of the Imperium of Man. Averted by even their fellow Guard regiments, they show a high degree of fatalism and an unusual morbidity of habit. Yet they are highly disciplined, morally reliable and self-sufficient soldiers.

The 42nd Siege Regiment had been deployed on Kheltan III to reclaim a supply route that had been attacked by the Eldar. A simple enough task for the stoic men of Krieg. But an ion storm attack and an innocent experiment by an alicorn from another world can make even the easiest of tasks much more difficult.

A Warhammer 40K/MLP:FIM crossover

Feeling restless at the dragon temple, the purple dragon of legend decides to take a leisurely flight one night. That all changes when a freak storm sends Spyro tumbling through a vortex and finds himself in a rather colorful new world.