Twilight Sparkle never seemed to notice Lyra Heartstrings. She didn't even remember Lyra's name.

They were friends back in Canterlot and even went to school together. Yet Twilight didn't notice that Lyra just happened to move to Ponyville the same day she did. She didn't even notice when Lyra appeared at her welcoming party. Nor did she ever seem to spot her old classmate passing by in the background on any other day during her stay in Ponyville. Some days she could look right at Lyra and never realize that they knew each other.

Lyra isn't a very noticeable pony. She has put a lot of effort into that.

Set in late season 5, after Amending Fences.
Note: Lots of spoilers in the comments.

Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

The Shaper is a smith of unparalleled skill, her creations the most sought after in the fallen world. When a pony named Lyra comes to her with a unique commission she has to put all her skill to the test to craft a weapon of great power. For Lyra's goal is not an easy one, and it is not just any weapon that can kill a Dragon.

A story inspired by this and this image, as well as this challenge by CDRW (whose fic A Still More Glorious Dawn Awaits is quite good).

Bon Bon's voice is funny, and that's about all that anypony who meets her notices, as her marefriend Lyra soon steals the spotlight with her explosive personality, strange obsessions, and curious beliefs. And why not? Bon Bon is, after all, a perfectly ordinary, boring pony in every way but two: her voice, and the carefully kept secret that she isn't really a pony.

(Edit:) Now with an annotated version, courtesy of the incomparable Shoggoth Lord!

Now Featured on Equestria Daily!
TV Tropes and a group of its own.
Audio version
( EPUB / MOBI )
Three Nights in Manehattan, a sequel
Hardcover Print-on-Demand Order Page

As a child, Daphne knew of a world where magic lived, where an immortal princess reigned over a beautiful kingdom, and longed to journey there beside Leit Motif, the filly she'd grown to love in the woods behind her home. But one day, when she needed her most, Leit Motif was gone, and she never came back to show her the way. As she grew, she put aside her childish dreams, and taught herself to believe the lie.
When forces beyond her knowing take her sister Amelia, though, she discovers that her childhood fancies were entirely too real, and is thrust into a journey that will take her back to that land she longed for, back to the childhood friend she'd abandoned, and to worlds she'd only dreamed of.

Interview with Pre-Reader Amacita
PresentPerfect's Review

Note- The story isn't that dark.

This story was written with my friend, Godzillawolf. After stumbling upon a homeless Trixie, Twilight tries to help her get a new job in Ponyville. However, an unexpected visitor to the town wants to leave Trixie homeless and feeding off scraps. Checker Monarch is set on ruining everything Trixie does, for reasons not yet explained. Trixie must discover new friends and must face this old danger through new eyes.

After escaping the Changeling gladiator arena at the cost of a friend's life, Equestria's lone human is attacked and befriended by Twilight Sparkle. This begins a long, strange, and confusing adventure to return home, and discover why he even arrived.

Complete, and edited twice... but If you see something I missed, I'd greatly appreciate it if you'd leave a comment.

Cover art made in Blender.

This story is a sequel to Of Kingdoms and Cutie-Marks

The Great and Powerful Trixie. Showmare. Illusionist.

Hunted.

With an artifact smuggler trying to kill her over incriminating information she found, she's been forced onto the road and towards the small town of Ponyville, where her destiny will clash with the town's inhabitants.

Including one pony originally from another reality.

A Skitchverse story.

Cover art by GatesMcCloud

This story is a sequel to A Skitch in Time (Revised)

The threat of The Collector has been vanquished, and peace has returned to the land of Equestria. Everything should be back to normal, right?

If only it were that simple.

The nations beyond Equestria's borders now stare at the sister monarchs with suspicion, viewing them as potentially compromised and dangerous; forcing Celestia and Luna to play international politics while they hurry to keep tabs on wards and prisons for dark forces long sealed away.

Meanwhile, the former human, now pony known as Skitch-Sketch struggles to find purpose in her life in Ponyville. Fear of other threats dominate her nightmares, and to make matters worse she will have to face her most deadly foe yet...

A mortgage!

Oh yeah, and her cutie-mark is fading away too.

The few.

The proud.

The only ones who were available at the time.

When the royal budget is blown, Luna needs to show that the disasters that have so drained Equestria's resources aren't going to continue. Reforming the Lunar Guard on a tight purse means that she doesn't necessarily get the ponies that she would have chosen, but how bad could it possibly be?

They're reckless, dangerous, they weren't even supposed to be here today, and they might well be Equestria's last hope.

(Featured and flattered!)