Inspired by the story image, RainbowDoubleDash's Lunaverse and Trinary's "Rainbooms and Royalty", I give you my take on the alternate universe concept. Namely, a universe where Spike is the pony and Twilight is his dragon assistant.

The thousandth Summer Sun Celebration is approaching. With it will come the return of Nightmare Moon. Celestia has no student to call upon to save Equestria, and is doing all she can to make the last day of peace meaningful for her people.

Meanwhile, Spike "Purple Prose" Flail is a reporter for the Canterlot Sun. He finds himself being shipped down to the boonies with his longtime friend and assistant, Twilight, to cover the biggest festival Equestria has seen in a millennium!

But even with a visit from the princess, there's no way someplace as boring as Ponyville could ever be newsworthy. Right?

A/N: Credit for cover image goes to dzetaWMDunion on Deviantart art.

Story would also include character tags for Thunderlane and Cheerilee if not for the character tag limit.

Now has a TVTropes page!

Twilight tries on her first pair of glasses, and though she enjoys them, something goes wrong. Anypony who merely looks at her faints on the spot, and she must figure out why before the entire city of Canterlot is compromised.

Cover art made by the talented and super cool MalWinters!

Now with a YouTube reading by Short Stories, and another YouTube reading by ZeusMacD

Princess Celestia: Goddess of the Sun, ruler of Equestria, beloved Princess of ponies. She is loved by all, and loves all in return. A calm and wise ruler, she sits on the throne in Canterlot, maintaining peace and harmony throughout the land.

What most don't know is that her past is much darker: She was once a commander of legions, a warrior and scientist of unmatched skill. Thousands of monsters and abominations fell to her forces, slain in the name of an old leader, one entombed within his own throne. Free of her old form, free of the powers of Chaos, she was cast into a new realm, in a new form, with a new lease on life.

She is the God Emperor, Eternal Ruler of Equestria and Lord of the Imperium of Man.

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Comments contain spoilers. YOU HAVE BEEN WARNED!!!

Twilight Sparkle wakes up one morning to find she's undergone some changes. She shortly discovers she wasn't the only one. (New cover art by Jamey4 on deviantart http://jamey4.deviantart.com/)

Warning, this work of fiction contains multiple fourth wall breaks, massive silliness, and more than a trace amount of alicorns.
The author may or may not have snapped at times in the writing of this work, and it shows. Bring a towel, you may get wet.

A Metroid Crossover

A meteor, resistant to magical manipulation, crashes in Equestria, Planet Equis, and soon spreads an unknown poison throughout the land. Containment is all but failing and the Princesses have little power to stop the spread of the Great Poison. The Elements of Harmony are of little use as no knowledge exists of this threat that consumes all life. Help comes from a certain Hunter, clad in metal.

Samus Aran will not only fight for her life as always, but her own sanity as well as these ponies that she begrudgingly starts seeing as allies. New horrors and abilities await her as a reason to fight slowly festers within her, possibly unlocking something she had been denied for so long: Friendship.

Notes and Resources:

This takes place after Echoes. The events of Corruption will have not happened yet. In terms of MLP, consider everything up to and including the Crystal Empire. Princess Twilight does not exist here, etc. The official Metroid Timeline can be found here.

As well, this story references the manga in many places. Reading of it is not required and I try my best to explain the context, but if you're interested, both volumes can be found here.

EDIT: This story was written over two and a half years, beginning in 2013. You'll probably notice the difference in writing as the chapters progress.

Pincer is a changeling, a proud soldier of Queen Chrysalis. After the failed invasion of Canterlot, he finds himself trapped and at the mercy of Princess Celestia's Royal Guard. Believing that Celestia sees his species as nothing but soulless monsters, he prepares himself for the worst. The weeks crawl by, marked by an endless series of questions he will not answer for fear of endangering his friends and family at The Hive. As his nerves wear down and his interrogators learn just how ruthless he thinks they are, they have nothing to report but his belief that they will kill and destroy his kind without mercy.

Celestia steps in to prove him wrong, and what Pincer learns leaves him questioning everything he has ever known — but also gives him hope for what he'd never thought possible.

Cover art commissioned from http://www.demonkings.com.

Now with a TVTropes page.

Reading an epic tale of one of the Third Hokage's missions, a 6 year old Naruto sets himself on getting some awesome summons of his own. Unable to find a contract on short notice, and not understanding why a contract is required, he goes through the necessary motions anyways and winds up in Equestria. Can Naruto convince the locals to let him be their summoner? Is the ninja world ready for the likes of Pinky Pie? Just how much will a young Naruto benefit from the Magic of Friendship?

After returning home from viewing a meteor shower, Rainbow Dash finds a green rock in her room that makes her violently ill when she touches it. As she and her friends work to find out what exactly happened, she will come to learn more about her past, her family, and her place in Equestrian society.

Cover Art provided by Supersheep64

Comments may contain spoilers. YOU HAVE BEEN WARNED!

After the defeat of Tirek, Equestria is safe once more, but Luna can sense that her sister is troubled. When Celestia retreats to the starry realm of ascension in order to look upon the past, Luna joins her to discover what is bothering her.

There is now a Spanish translation of this story, courtesy of Spaniard Kiwi

When Wreck-it-Ralph finds a villain character who seems to have gone Turbo, he finds more than a handful in the handful sized sprite.
For one thing, she has no idea what game she comes from.
For another, her code seems completely foreign to the Arcade.
For a third...she's absolutely adorable.
Having only just finished cleaning up after King Candy's mess, this little Nightmare could be a problem...or the greatest blessing Ralph has ever received.
And shadows from the past move behind the scenes...

Part of the PWNY-verse.

Edit: Now with cover art by KittyCoverArt.
Edit: Now with fan art at the end of the first chapter.