A train accident robs Rarity and Sweetie Belle of their parents, forcing the sisters to live together. Now Rarity must put her generosity to the test: balancing her career at the Carousel Boutique while being the mother figure Sweetie needs.

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

Diamond Tiara needs a little more help changing her ways. She used to be a bully at her school, but now she's a changed pony.

However, is change really that easy?

A simple fable for ponies to tell their foals at night, that's really all it was. But one must wonder: where did the princesses really come from?

The world is about to end, but Granny Smith is havin' none of that now ya hear?
The Amulet of Bemethus has chosen Granny to save the world, and points her off in the right direction. Watch in amazement as Granny Smith puts the world in its place, and reminds it to call its mother every once and a while.
Armed with nothing more than her wit, and a devoted but skidish orderly who makes sure she takes her meds on time, she travels across Equestria giving everything a thorough lecture.

The girls face old threats and new methods of madness, when a strange force pulls a new friend into their land. In a startling crossover, the Captain of the Starship Enterprise finds himself trying to adjust to a VERY different culture, while the residents of Ponyville try to understand his presence. When his presence coincides with a dangerous sign in Canterlot, Twilight and the Captain both begin to put the pieces together, and come to a realization. With little more than suspicion to go on, they seek their friends, and attempt to remedy the situation, despite strange obstacles and hidden information. While the Captain and his new friends struggle to confront their old enemy, he also seeks to find a way back to his ship. With his new friends, he may learn more than just a way home.

I started this fanfiction a while back, and long before I knew about the new "Keep Calm and Flutter On" episode; so keep in mind that this is to take place before the events of that episode.

Dear Princess Celestia, this is easy!

Join Twilight Sparkle and her friends as they easily defeat every challenge thrown at them with their awesome friendship powers.

Based on this story:
My Little Pony: Friendship is Overpowered (Equestria Girls)
My Little Pony: Friendship is Overpowered (Season 5)

This story is a sequel to My Enemy's Enemy

Rainbow Dash is staying in Canterlot for a few days to perform in a Wonderbolts show, and she decides to take Scootaloo with her. Scootaloo finds herself becoming a celebrity of sorts at Central Canterlot School and begins basking in her new-found glory - but she soon notices a young changeling, Pupa, is being left out and tormented by the other students. Will Scootaloo be forced to put her popularity aside to help a filly in need?

(The prequel isn't necessary reading, all you need to know is changelings and ponies aren't enemies anymore, and the changelings live in Canterlot now, alongside the ponies :3)

When new princess Twilight becomes curious of Celestia's history, the elder princess reveals to her a story older than time, and with it surprising secrets and details of their world's past.

When Pinkamena was a filly, a Sonic Rainboom knocked her in a deep coma; one that doctors came to believe she would never emerge from.

To her, though, the event made her believe that her purpose in life was to spread joy. She no longer lived the dull, boring existence of the rock farm. She was the happiest pony in Equestria where everypony was her friend.

But now as she miraculously wakes up from this trance, she is hit with the cold reality.