First of the Savage Skies series.
After running afoul of timberwolves in the Everfree Forest, Fluttershy is saved by a mysterious young colt with a most unusual and disturbing feature. Realizing that he is alone, without anyone else to care for him, Fluttershy realizes that she must try to bring this lonely foal out of the forest and give him a life of love and friendship. The problem is that this colt's...unique qualities have made him more than a few enemies, including some who are closer to home than Fluttershy realizes.

Now with a sequel: The Promise of a New Day.
Now with a TV Tropes page.

Twilight Sparkle, Celestia and Luna are transported into a strange alternate Equestria, the Land of Always Summer, where the day lasts forever and a terrible queen rules with an iron hoof.

Feel free to check out or add to the story's TV Tropes page.

This story is a sequel to The Irony of Applejack

Warning: this story is a sequel. Therefore, it is highly recommended that you read the prequel first before continuing!

Over half a year has passed since the changeling attack on Ponyville, and Applejack would like to think things have finally settled down. Much has changed for the young changeling, and all of Equestria in kind. The new district in Ponyville proves that, along with the town's many new residents.
But there is much the young queen does not yet know about being a changeling. Some things, she will learn, can be chosen, while others will be chosen for her. With new allies and enemies emerging all around her, Applejack must discover what it truly means to rule before the choice is taken from her forever, and the history of the changelings repeats itself, once again...

Image provided by Heilos.

For most of Applejack's life, she didn't know what she was. True, she understood who she was well enough.
But ponies don't change shapes, nor do they get strength from love.
Applejack never thought too hard on it... until the events of a certain wedding brought about some harsh realizations.
Now, with Equestria still reeling from the surprise attack, will Applejack manage to come to terms with what she is? Will she even be able to keep her secret safe?
For if the royal guards don't get her first, the conspirators in the shadows just might...

Image provided by Heilos -

The world is full of life, full of light. Yet all life must end, all light has shadows. The world is a place of contrast. These exist naturally, and cannot be stopped. Yet there are those who embrace the shadows, who hate the light. There are those who have abandoned life, and made death their mission.

In the world of peace that Aurus Marz, new king of the changeling nation, seeks to create, these creatures have no place. Yet they cannot be easily stopped. The darkness that rebels against the light of his vision of a bright future will prove a strong adversary.

When assassins come again for the young king and his many ambassadors, it will fall to one of their own to rise against them, and bring them to justice.

This is the legitimate direct sequel to Visionary.

Meet Lavender, a rare offspring brought into the world by a loving dragon and a beautiful pony. She is told constantly by her parents that she is a beautiful gift of nature, but she is reminded everyday about just how different she is from the rest of the world. She is going to learn very rapidly how cruel and unforgiving the world can be for anything different from them.

Follow the journey of Spike, Rarity, and their offspring Lavender from birth to adulthood as they try to survive prejudice, natural impulses, and even their relationship between each other.

The character of Lavender and the artwork included all belong to Carnifex
_________________________________________________________________________________________________________________________________
Someone actually thought this fic was worthy to be in the Twilight Library. Well... if you say so.

It really hasn’t been a great day for Discord: First his appendages mutiny, then he discovers that he’s got a conscience, and if to add insult to injury, Celestia suddenly wants him to babysit her little sister on her adventure to rescue the changeling race. As if he didn’t have anything better to do! Can you imagine it, the spirit of chaos trapped in a land which is full of nothing but sand, stone, and historical ruins? To immortals, however, history is but another word for their own past.

Join us as Discord reports this high strutting tale, full of excitement, forgotten treasures, exotic cultures, romance, and not to forget a sizeable deal of chaos.

---
Sequel to White on Black, but if you're ready to accept some weirdniss in the beginning readable on it's own.

“You are hereby invited to the wedding of her royal majesty Princess Celestia of Equestria.”

Strange, as far as Twilight Sparkle was aware, Celestia didn't even have a special somepony let alone a fiancè. Well here's the good news: She doesn't have a special somepony. Bad News: Chrysalis isn't a pony.

What happened between the Goddess of the Sun and the Conduit of the Swarm-mind? Is it just another plot to take over Canterlot, or might there be more under the carapace of the queen than anybody expected? Well, we'll never find out if nobody stops her and Twilight from killing each other first...

----
Click the little source thingie under the cover image cause Karzahnii is an awesome guy.

Also special thanks to Wise Cracker, and MrJoshy, who always endure me pestering them with my story. :P

Set in the conversion bureau meta-verse, Landfall covers a time of great upheaval as Equestria makes contact with land for the first time.

The story follows Smith, a human that is struggling to find time to undergo pony transformation but with the magical barrier now clearly visible the choices are very limited.

Orphaned from birth, with only the memories of a soft touch and gentle voice to remember her by, Twilight yearns for her mother. What pony wouldn't want to know why they were abandoned, why they were left to be found by the Princess of the Sun herself.

That was nearly two decades ago though. Twilight was older now, and hopefully wiser. She is happy with her two best friends, Cadance and Shining Armor. They are like family to her, the brother and sister she never could have. Though dreams still haunt the young mare, dreams of lullabies and tender kisses, she has moved on.

The personal servant to the Princess of Helios, the land of the Sun, Twilight enjoyed both rank, and knowledge. But it also means that when Princess Luna comes to visit her old friend, Twilight is given the task of tending her. The Princess has come in search of marriage, at the behest of her ruling Council. They demand an heir to ward off the potentially catastrophic attacks of the neighboring dragons.

Soon, Twilight will be tested and tried. She will be given the a choice between the life she has known, and the duty she is sworn to. But never, not once, will she forget.

For who can stop loving their mother.