A reboot of Waking Nightmares, taking the story in a different direction.

Celestia has been suffering from nightmares and her sister Luna cannot seem to stop them. Alongside this, the dreaded Queen Chrysalis has been caught and is finally standing trial, several world leaders attending to help decide her fate. On top of all this, nine ponies and a dragon have appeared, claiming to have been transformed and sent to Equestria by an insane wizard.

What else can go wrong?

Equestria is still picking up the pieces after the defeat of Tirek, and everypony is helping out with the paperwork, even Rainbow Dash. Things change when Princess Celestia arrives, bringing with her a letter with some very stunning accusations of the exploits of a resident in the town of Oasis. Now, the main six are tasked with finding out if the letter was truth or fiction. Did this Mister Baker really do what they claim? Only one way to find out.

However, Mister Baker is not who, or what they expected.

Rated Teen for occasional language. Additional tags added for more dark themes.

Proof read and edited by the amazing SunnyPack , Snakeskin Ducktape, and Tyrannosaurus Tux.

A thousand years after the Princesses disappeared from Equestria, Twilight Sparkle meets a lost Cloudsdale scout named Rainbow Dash. Together they look for a way to end the thousand-year night and dispel the darkness that has spread across Equestria.

Edited by Pascoite
Contains fairly mild grim-dark. Inspiration taken from the Dark Souls games, but it's not strictly a crossover.
Chapters titled "Arc #: Chapter Name" are part of the main story. Chapters titled "Character: Chapter Name" are one-shots about other characters, set in the same world, and aren't necessary in order to follow the main story.

This story is a sequel to The Stolen Gem

They say that if you ever get lost in the Everfree forest, you may hear her singing. When you do... run.

After the Heartstone incident, Twilight Sparkle finds herself in need of a new direction; a new purpose... not to mention a new place to stay. A bolt of inspiration sets her and her new-found friends on a path that leads deep into the heart of the one place everyone knows you should never go...

Part II of Legend of the Six; a humanized fantasy-adventure that draws heavily on the mythos and lore of FiM to create a new and exciting tale of action, intrigue, and of course, friendship!

Cover art modified by the Great and Powerful MelloReflections; original was created by the amazingly talented bill-yi!

[Complete! With TVTropes apparently!]
Also, apparently, an animated trailer.

In a world of brass and steam, Twilight Sparkle had thought she had made a life-changing discovery with the invention of the telescope. For better or worse, she was correct.

Now her discovery has not only changed her life, but the lives of those she seeks out in her desperate attempt to contact the only other creature as lonely as Twilight herself.

It all would have been much simpler, but it had to be the one Twilight could only call The Mare on the Moon.

Decidedly not within walking distance, then.

[Featured on EQD before story was meant to be submitted. 4/03/2015]

[Editing team: Southpaw, Wolfvenom, Maskedferret, SwanSong and BluePaladin42, without whom this story would be a fraction of its current state.]
[Special thanks to Novel-Idea for the updated cover]

It has been one of the closest guarded secrets of Canterlot's royalty. Deep in a specially constructed dungeon, surrounded by warding spells and powerful magic barriers, exists an enigma. Within a cage that could only be described as something out of a nightmare, it waits and watches all of Equestria. A creature that cannot age, is immune to disease, does not thirst nor hunger, and resists all injury. But, it also holds secrets and knowledge that could safeguard the kingdom. Its powers are frightening, but it is civil enough for debate when patience permits.

Princess Celestia has sought counsel with the creature before, enduring it making deal after deal for its services. The Princess walks a fine line when dealing with it, knowing full well anything could give it an advantage despite its imprisonment. She has had to go back on her word in these dealings, and from this a deep animosity between them has been born. It is a necessary evil as she is convinced this is a being capable of untold evil far and above anything Equestria has ever dreamed of. So long as it remains within the confines of its cell, her kingdom is made safe. So much magic has been woven to ensure that, there is little chance of escape.

So long as the magic holds, there is no danger. So long as the cage remains strong, the nameless creature stays enthralled in his cavernous dwelling. If that were to change--if the magic failed--not even the wisest could say. But one thing is assured, it does not bode well for Equestria.

Have you ever heard of a mare named Faust? She's an Alicorn, just like the Princesses, but not a princess herself. Some say she's a queen, some say she's their mother. The truth, well... she's really overworked. And with her duty as The Equestrian Archivist she has a pretty demanding job. But what happens when this overworked alicorn decides that she wants to take a vacation in Ponyville? Furthermore, what'll happen when she skips out on her job to take that vacation?

(My first story! A different take on Fausticorn, I've seen her given a general persona that just doesn't seem like what I saw in the original art. So here's my idea of what she might be like. Tags will be added as the story continues.)

HOLY.... F-Featured on December 21 2014! Thanks guys! That is amazing!

Edited by the lovely PhiliChez

Now with a TVTropes page!

A strange blue box crash lands in the middle of the Everfree Forest to be discovered by Twilight and Spike. The Doctor stumbles out of it and makes the shocking discovery that he's accidentally traversed to another universe entirely! Ready to test his new four legs in this universe, the Doctor does what comes naturally to the renegade Time Lord; jumps cutie mark first into danger.

With Twilight Sparkle and the other Elements there to make sure he doesn't do anything too stupid, the Doctor with his TARDIS goes off to explore everything this new universe has to offer. New adventures and historical ponies await the crew as they continue to go onwards and upwards.

Cover art by: http://bakki.deviantart.com/

Brilliant isn't it? Check it out! (slightly NSFW)

Once, she was a prisoner, beaten and tortured by grotesque horrors.

Once, she was an honored knight, decorated and respected as the strongest of warriors.

Once, she had touched godhood, revered as divine by the people.

And once, she was even a coward, running far from her responsibilities.

But what is she now? Lost, broken, alone, fallen? She is all of these things, but most importantly she's alive.

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When Big Macintosh finds an injured pegasus mare in the Apple family's new barn, he and the rest of his family take it upon themselves to see her back to full health. Soon, they see that the mare carries with her an aura of mystery thicker than anypony could ever imagine, bringing with it both new adventure and enlightening experiences.

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A Magic: The Gathering and MLP crossover. I don't own them, Hasbro does.
Editing by Alovelylittlecomplex and Dark Tendencies

Featured on 8/7/2014. Thank you everyone for the support.

Twilight has developed a device that can detect strange signals coming from outer space; signals from aliens! She gathers her friends so that they can all listen in.

But they may not like what they hear...

cover image courtesy of DocWario

I'd appreciate if everyone could keep the YouTube embeds in the comments to a minimum. The sheer number of them is putting a bit more strain on my connection than I'd like. I'm going to start deleting any comments with 2 or more embeds in them.