When Octavia and Vinyl Scratch decide to combine their respective musical styles into a new genre that will celebrate not only their talent, but also their unique bond, they feel confident that they're the pioneers of the new age. So when the two find their music challenged by another pair of musicians, they set out to make sure that theirs is the best. However, the rival two aren't bad artists themselves, not to mention they’re certainly not… of the same persuasion as Vinyl and Tavi. In the snow-wrapped streets of Manehattan, can they risk exposing their new found -and still taboo- relationship, or will they be doomed to second place?

Incredible cover art by JackiePhantom13! DA: http://jackiephantom13.deviantart.com/

EQD!!
Link: http://www.equestriadaily.com/2012/04/story-mixing-relationships.html

After getting their Cutie Marks, the Crusaders never really did anything much. Soon, they drifted apart. But what happens when Scootaloo finds their old clubhouse...

An ancient evil escapes from its prison... A familiar story for the bearers of the Elements of Harmony, but against a threat even older and more alien than Discord, victory will be no simple thing. Even so, with friends rallying to their aid and a former rival fighting by their side, in this strange aeon even death may die.
A Cthulhu Mythos crossover.

This story is a sequel to Twilight Sparkle vs. Bridle-Zilla

On the morning directly following Lyra & Bon Bon's wedding (See: 'Twilight Sparkle vs. Bridle-Zilla'), Twilight wakes to find an unexpected guest in her bed. Hijinks ensue.

What was originally meant to be a single piece, this story, its prequels and sequels, focus on the mane six and their dealing with being the Elements of Harmony, how ever long that will last...

Be Awed and Amazed by the tale of Sweetie Belle as she traverses the multiverse in search of her lost mentor and friend, Twilight Sparkle! Will she find her in post-apocalyptic Equestria? Or maybe in a strange world where everypony is the wrong gender? Or even where a Pony claims to be a human? Read as she journeys through very familiar worlds you might have read about... if you dare!

At this point in time all the main worlds to be visited have already been chosen. Thank you all for the suggestions, and I hope you enjoy the surprises!

Here's the official TSC:F Music Intro: The Sweetie Chronicles: Fragments

WDTP: S2/3-CE
You can also visit the TV Tropes Page which has spoilers!

After discovering a long-lost artifact, Daring Do is suddenly thrust into a world of deadly danger and intrigue in the most hazardous jungle of all: Manehattan. However, she soon finds an ally in a pony clad in purple and going by the moniker Mysterious Mare-Do-Well. Together, the two mares endeavor to uncover the truth behind the artifact and the ponies that want to silence them...forever...

(Now with Fanart!)

Scootaloo's rather embarrassed by her Mom. Not because she isn't cool, arguably she's both the hottest and the coolest mom in Ponyville. It's not about the fact that her mom serves on the royal court either, though that doesn't help. Maybe it's got more to do with the fact that the reason her mom is almost never seen after sunrise or before sunset, or because before the Mare in the Moon returned to Equestria, she knew her name.

Or, you know, that her mother is a chocoholic, an embarrassing know it all that's actually lived it all, owes personal favors to Princess Luna, and has the unfortunate job description of 'ruler of the land and day'. Sure, having Celestia as your mom is cool and all, but at the same time nopony can know who she really is. Nopony gets to 'know' her, and every moment is guarded against snooping visitors. And yet, there's still hope for a better day to come. Even when all your mom's enemies and rivals finally come home to roost and ruin your day. It can't be all bad, right?

Now with a Trope Page: Scootamom on TVTropes

And Fanart:
[img]http://fc04.deviantart.net/fs71/i/2012/266/8/9/scootamom_by_familywing-d5fnnov.jpg[/img]

When Ruby boards the first trans-oceanic flight in Equestrian history, the last place she expects to end up is stranded in the middle of Eternity's Crossing in the wake of a horrific zeppelin crash. After a mysterious tower leads her and a fellow survivor to discover a twisted and fragmented city twenty thousand feet below the surface of the ocean, though, a bit of fire and smoke is the last thing she needs to worry about. Between the horrendously disfigured residents and the paranoia of the madmare who once built and controlled it, daily survival in this corrupted utopia is anything but a guarantee. But with the help of some new friends and a few genetic enhancements, Ruby isn't going down without a fight, and in the process might just discover that the deadliest weapon in Harmony is herself.

An adaptation of BioShock for the world of MLP. Written to be comprehensible to anyone, regardless of whether they've played the original game.

Two months after the events of Yellowstone, Wild Magic from Equestria has run rampant throughout the rest of the world, resurrecting ancient horrors from around the globe. Mysterious and terrible monsters of myth threaten to exterminate both mankind and ponydom! With the blessing of Princess Celestia, Twilight and her friends reunite with Agent Hawk and his team to combat this new terror before it destroys the world!