Lazy Pines is a small town in the high country of Colorado, easily overshadowed by the bigger sights to see along Colorado State 9. When influenza strikes the town hard, it is little more than a statistical blip in a typical flu season. No one thinks any more of it as the initial wave of infection passes ... until the other symptoms begin to manifest.

Meanwhile, during what should have been a routine trip to Canterlot, Twilight Sparkle stumbles upon a strange anomaly which turns into an all-consuming mystery. As she discovers the complex web of magic stubbornly maintaining this mystery's secrets, she grows worried what it could mean for herself and her family.

And as the residents of Lazy Pines struggle to understand -- or even believe -- what is happening to them, two worlds have irrevocably been set on a direct collision course.

Updates every other weekend.

Cover art by Mix-up. Please check out more artwork by this talented artist.

Now has its own TV Tropes page thanks to redandready45.

Twilight Sparkle has too much magic, and it will take her decades to learn to control it. Her spectacular loss of control during her entrance exam only proves that fact. She is a danger to herself and others.

After Sunset Shimmer’s disappearance, Princess Celestia needs a new student to bear The Element of Magic to defeat Nightmare Moon. With all of Equestria at stake, Twilight Sparkle…is not the pony she needs.

Princess Celestia seals Twilight Sparkle’s magic with the distant promise of one day teaching her.

But there are two diarchs of Equestria. Amidst a lucid dream, an offer is made.

“Hello, Twilight. Would you like to be my student?”

Cover art provided by Lafiir.

[Complete! With TVTropes apparently!]
Also, apparently, an animated trailer.

In a world of brass and steam, Twilight Sparkle had thought she had made a life-changing discovery with the invention of the telescope. For better or worse, she was correct.

Now her discovery has not only changed her life, but the lives of those she seeks out in her desperate attempt to contact the only other creature as lonely as Twilight herself.

It all would have been much simpler, but it had to be the one Twilight could only call The Mare on the Moon.

Decidedly not within walking distance, then.

[Featured on EQD before story was meant to be submitted. 4/03/2015]

[Editing team: Southpaw, Wolfvenom, Maskedferret, SwanSong and BluePaladin42, without whom this story would be a fraction of its current state.]
[Special thanks to Novel-Idea for the updated cover]

In the aftermath of her battle against Tirek, Twilight Sparkle is unwell. She wants more. She needs more. And she is afraid of what others might think of her.

But even in the midst of her growing despair that she has betrayed everything she stood for, she learns something about friendship and what it means to be an alicorn.

Celestia and Luna were born as unassuming foals in troubled times. But already marked for greatness, the simple earth ponies stand to face a world set against them, full of danger, fear, and sadness. A world they will change forever.

A sweeping epic taking place before Equestria was made, where Celestia and Luna must rise from normal foals to become the Princesses we know them as, beset from all sides by monsters, other ponies, and even the forces that govern nature. Their tale is as tragic as it is triumphant.

Currently on hiatus. For more info, go here.

(Cover and internal art by Madmax)
(Editing credit predominantly Lightside Luc)

For almost a thousand years, the immortal Nightmare Moon has reigned over Equestria as Empress. To the average pony, Nightmare Moon is an overarching enigma whose rule is absolute and whose wrath is terrible. But to Twilight Sparkle, who as an orphan has never known her parents, the Empress is something else entirely. When the young unicorn is brought under the royal wing as an apprentice, she learns a great deal more about the supposed tyrant than she ever knew. But as Twilight is introduced to life with her new mentor, she is thrust into a world of political intrigue, conspiracies and secrets. Secrets that were never meant to be revealed. As allies and enemies plot against the very peace of the nation, will Twilight fall prey to the perils of her new position? Or will she prosper and find in Nightmare Moon the mother she never had?

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My eternal gratitude to my editor, LordOfTheWrongs, without whom Night's Favoured Child would not be the story it is today.

Now with added TVtropes!

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

Summer is the perfect season for things that grow. However, growth needs fuel, warmth can burn, and romance can be the most volatile fire there is. After she leaves Ponyville and lands a job as a city guard, Gilda will have summer days that are filled with lessons of growth, of love, and of pain.

This is a continuation of Heart of Gold, Feathers of Steel. I recommend reading that story first.
This story is concluded in Evening Flames

Special thanks to WentoX for this awesome, custom cover.

Friendship lasts forever.

Right?

Three years ago, Gilda and Rainbow Dash became fast friends at Junior Speedsters' Flight Camp. Time took its toll, though, and the pair drifted apart.

When Gilda tries to reconnect with her not-so-long lost friend, she'll discover that things can change a pony after three years: a new home, new job, and new friends.

This story continues in Summer Days

Title Image Credits
Original: http://mallorysbeast.deviantart.com
Coloring: Bandit (no link available)

Tensions grow hotter in the mining town of Farrington after the events of one disastrous night. The fallout from this blaze will test many citizens' relationships in fire. Some will falter, but some may perservere.

Before any repairing can begin, ponies—and one griffin—will have to take stock of their pasts, or else their futures may end up strangled by their scars.

Note: This is a sequel to Summer Days. I strongly encourage reading that story first.

Special thanks to Gaiascope for this awesome cover!