Source

After an accident, Rarity and Twilight are thrown in a race against time to stop their transformation into changelings before they become part of Chrysalis' swarm forever.

Source

My name is Twilight Sparkle, and 350 years ago, Sweetie Belle and I vanished without a trace.

Now here we are, in the future.

Equestria has become a utopia, with everypony living in peace and harmony.

Everything is perfect. All a pony could ever want, and more.

My name is Twilight Sparkle, and I want to go home.

Editing provided by Stereo_Sub.

Cover art courtesy of Geomancing.

As seen on Equestria Daily.

Source

After the changelings' failed invasion of Canterlot, Twilight tries to soothe some of Ponyville's rampant paranoia by casting a spell to prove there are no imposters hiding in the town. But her spell leaves her in an alien body, facing a mob of angry ponies who just don't believe her when she says she is Twilight Sparkle.

Or, at least, she was Twilight Sparkle, anyway...

Featured on Equestria Daily, 2/17/13

Cover art is by the awesome and amazing Conicer

Twilight discovers Discord in-hiding - which is strange enough - but the discussion they have causes her to consider the particulars of true harmony, and whether or not a being such as he should be allowed to live freely to retain his part in it.

Slightly shippy and possibly angsty. Putting it under 'sad' because there's no 'hurt/comfort'.

This is an idea that wouldn't leave my head, inspired by Fairy Slayer's "Mommy Nearest," Aldea Donder's "Alicorn," SoundofRainfall's "Play" and RainbowDoubleDash's "Lunaverse"

Alternate Universe: Instead of Twilight Sparkle, Princess Celestia made Rainbow Dash her personal student instead! Follow her through the events of the 1,000th Summer Sun Celebration. A reimagining of "Friendship is Magic"

Source

The supernatural: Ghosts, zombies, werewolves, spirits.....   vampires......

Twilight Sparkle always thought that the supernatural was just a bunch of superstitious nonsense, just some scary stories to tell around a campfire. She couldn't have been more wrong.

After an occult ritual gone horribly right, Twilight finds herself among the ranks of these so called 'myths', whether she likes it or not. Due to the same force that changed her, dark shadows have begun to spread across Equestria, bringing to life these ancient fairy tales. And Twilight might just be the only one that can stop them...

For better or for worse, Twilight has been changed. Will she embrace this dark gift and become the hero Equestria needs, or will she eventually succumb to temptation and become the very thing she fights?

Source

Some accidents are small, and some endow you with the power of a godly ruler. On the opposite end of things, you lose your wings and your ability to move celestial bodies and you can't tell anypony, because what would they think? It's OK. Twilestia just needs to get to Canterlot and switch back with Tiasparkle before revealing their identities. But why not have some fun along the way?

Rated teen for shenanigans and some more serious parts.  Takes place at the end of lesson zero. Please tear this apart with comments. I like criticism.  

If somepony could do cover art that would be great. If you are confused at any point, make a comment that helps me know why.

Source

In a moment of weakness, Chrysalis had more than a taste of Shining Armour's love. 11 months later, Twilight Sparkle finds herself a brand new niece by way of 'A small foal in a basket on my door step'.

Special thanks for the picture by Awilldrawforfood1

Now edited with DoomManta.

After an unknown accident Twilight Sparkle and Rainbow Dash awake to find themselves sharing the same body! Now they must struggle to hold themselves together as their world is turned upside down. How long can two ponies exist in a single mind? It’s a race against time as they search for answers before it’s too late. When all is said and done, you’ll never look at Twilight Dash the same way again.

(Parody) Kate the college student loves ponies. But unwanted magnetism to her own gender has also made her a bit of a homophobe. Landing smack in the middle of Ponyville, she discovers (to her horror) that she is even more attractive to mares than she is to women. Her mission? Find actual friendship without being shipped. Whether or not she's successful... is entirely up in the air. A fun reversal and satirical poke at HiE tropes with heart to spare. As a small warning, while the story is not particularly explicit, there is quite a bit of innuendo which is played mostly for laughs.