*HIATUS UPDATE 10/15/2018: There is currently no set schedule for the remake of this story, but I assure you that it still has not been canceled. I get regular comments, favorites, and emails that all point towards this being a beloved story worth finishing, so one day I will do just that. Thank you all for your time and patience!*
Ever since they were little colts, the Flim Flam brothers had a dream; a dream to make a wondrous machine to set their lives on the fast track to success. The machine, known as the Super Speedy Cider Squeezy 6000, was missing just one component to make it all complete. Just one elusive item that no sane pony or pony with values would ever consider using:

Fresh dragon's breath.

Guess what I am.

I was taken from my home, my family, and my wings were slashed. I am no longer a person, I am simply a cog; a cog in the Super Speedy Cider Squeezy 6000.

This is the beginning of my wonderful tale.
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Honorary pre-reader as of chapter 10: aiovas. Official Editor: Thardoc. Thanks go to dmkamikazee of deviantart for cover art A! Thanks go to More Dakka for cover art B! A fan created art gallery for this story can be found here on my homepage!

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

The glamorous unicorn Opalescence is haunted by bizarre recurring dreams of a world in which she and her friends are all animals. But as vivid as these dreams are, surely they're just dreams, right? There couldn't actually be a parallel universe somewhere where they're little more than pets ... right?

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

Princess Celestia tires of constantly being surrounded by decorum, deference, and formality, and decides to take a day off from being Princess. But visiting Ponyville incognito is harder than she expects. Will she be able to fit in and make friends without blowing her cover?

The Cutie Mark Crusaders ask Rainbow Dash and Fluttershy about what happened just after the events of the Cutie Mark Chronicles; specifically, what happened to Fluttershy and Rainbow Dash immediately after the race. Reluctantly, Dash and Fluttershy delve into a tale. A tale of a young Fluttershy's amazement at the world she had landed upon, and a filly Dash's desperate quest to save her from that most evil of places: THE GROUND.

The Sequel to Number 12.
The Doctor and Twilight leap into the future, though it may be a far darker place than they envision. In the mean time somehow the Doctor keeps crashing around Ponyville, something to do with Fluttershy, but what?

Twilight and her five friends are transported during a botched spell, across dimensions to... Ponyville, Equestria? But not the same one that they knew. Sitting on a bench is Harpsy and Babar. The Doctoress avoids apples from an aspiring Applebuck. And in a library across town, six stallions join their forces as they try to decipher the appearance of filly look-alikes of themselves around Ponyville!

After hours at the Sugarcube Corner, a heavy storm thundering outside, Pinkie finds a pony knocking on the door.

Featured on Equestria Daily.

Twilight is invited to Canterlot to compete with some of the greatest magicians in the world for the Moonstone Cup, a prestigious award for the most powerful and skillful magicians, unicorn and otherwise. Can she win? What sort of competition will she face?

Awesome cover image was taken from NoOneBahtim