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

All of Equestria is united in celebration for the return of their beloved Princess Nightmare Moon. But when Celestia and everypony else recieve her she's skeletally starved, filthy, and very nearly dead. Meanwhile, while everypony's eye is turned, a lusty Blueblood pursues Twilight Sparkle, intent on adding her bloodline to his own so his family might step closer to godhood. (Alternate Universe, there never was a Princess Luna)

Dash has a secret. A secret that could cause an old enemy to return. A secret that Dash herself is not even aware of. The element of loyalty and their friendship is put to the test as Dash's life changes in one small moment.

...
Does contain a shipped couple.

Dusk Shine has dealt with many trails throughout his life. From clashing with Nightterror Nebula to outwitting the mischievous Eris to thwarting King Nymphamos’s invasion, he'd seen it all.

All in all, Dusk Shine would admit that life was hardly easy. And now, Dusk finds that his mentor's self loathing is the least of his problems as he finds himself thrust into a world where he and his friend... are mares?

edited by Saylux and OverlordCornutt

Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.

An archeologist finds himself pulled into a parallel world by Discord's storm of Chaos, and encounters the mysterious creatures that live there. How will a rational human, confronted by creatures out of mythology, and unable to find his way home, adapt to his environment? Only one way to find out.

Ace was a street magician with a lucky streak. His luck was legendary among casino owners and fellow magicians. Any risky trick would succeed flawlessly and any gamble would pay off for him.

After performing his greatest and final trick he is brought face to face with the entity responsible for his incredible luck. The goddess of fortune herself. Lady Luck.

She offers him a deal. To become her champion, her Wild Card, and go to Equestria to spread luck among those who need it the most. So he finds himself in a magical land, in a new form, and ready for anything that comes at him. To a reasonable degree.

(Part of the Chess Game of the Gods universe created by Rust and BlackWing)
(Cover art by Grusborg on deviantART)