This story is a sequel to Rescue on Diamond Mountain

Story seven of the Savage Skies series. The first months of Dawn's stay in Ponyville have been tumultuous, to say the least. Fortunately, winter is coming, not only offering the colt respite from his enemies, but also giving Dawn the opportunity to enjoy the season with his new friends and family. Little does he know that this is to be a season of many firsts for him.

Meanwhile, a new pony has come to Ponyville in response to Twilight Sparkle's call for research subjects. Unfortunately, this stallion's past experiences have left him bitter and paranoid. It will be up to Rarity, of all ponies, to make this unexpected guest feel welcome in Ponyville and heal the wounds in his heart.

This story is a sequel to Shadow of the Sun

Story 5 of the Savage Skies series:
Autumn has arrived in Ponyville. The harvest is in full swing and all is as it should be. After enduring the trials of the past few months, Dawn Lightwing is looking forward to what promises, hopefully, to be a peaceful season before a tumultuous winter. However, the coming season has the unwelcome effect of bringing his enemies closer than he feared. However, he is fortunate to have a loving family, good friends, and somepony who is maybe more than just a friend.
The series begins in Foal of the Forest.
Now with a TV Tropes page.

This story is a sequel to Seasons Turning

Story 6 in the Savage Skies series.

Thanks to Twilight Sparkle's plan, Dawn Lightwing's story has been spread across Equestria. Back in Ponyville, Dawn and those close to him prepare for the inevitable fallout. However, their plan has some unexpected consequences, leading to Dawn's place in Ponyville coming under threat in the most unexpected of ways as Fluttershy must prove her fitness to be Dawn's mother.

However, there is something more at work behind the scenes. In order to protect his home and his place in Ponyville, Dawn must venture abroad with an unexpected and unwanted ally in order to bring an end to these machinations.

The series begins in Foal of the Forest.
Now with a TV Tropes page.

This story is a sequel to Storm on the Horizon

Story 4 of the Savage Skies series.

It is well-known that the brighter the light, the deeper the shadow. Princess Celestia is unquestionably Equestria's brightest guiding light. Unfortunately, two ponies must deal with the very deep, very dark shadows that she casts.

Dawn Lightwing has overcome many trials since moving to Ponyville. However, his past and the ponies that haunted it are not as far behind him as he would like to think. Whether he likes it or not, his enemies, who draw their hatred from their irrational reverence for Princess Celestia, have found him again and he must struggle with the fact that his mere presence could a threat to his friends and his new family.

Twilight Sparkle must deal with a different shadow as she travels to Canterlot in order to learn more about the mysterious Eyes of Nightmare, as she must contend with the Noble Court, who live in the shadow of the Royal Palace itself, its members planning to use Twilight and her friends to advance their own ambitions, stopping at nothing to have her under their influence.

Thankfully, neither of them will have to deal with these obstacles alone.

However, something even more dangerous is stirring. Dark matters are afoot.

The series begins with Foal of the Forest.
Now with a TV Tropes page.

This story is a sequel to Foal of the Forest

Second story of the Savage Skies series:
Dawn Lightwing has overcome many trials in his life; persecution for his unique eyes, living amongst the monsters of the Everfree Forest. But now all of that is behind him. He's been adopted by Fluttershy, mended from his conflict with Applejack, and now sits poised to go to school and live the life of a normal foal. Unfortunately, Dawn's past is not so far behind him as he would like, as his experiences have left scars on his mind and heart that threaten everything he has gained since coming to Ponyville.

Followed by Storm on the Horizon.
Now with a TV Tropes page.

This story is a sequel to The Promise of a New Day

Story three of Savage Skies:
All sorts of things are brewing in the pegasus city of Cloudsdale, which is a problem for Ponyville as the one thing that isn't is a rainstorm. As the drought continues to drag on, Rainbow Dash must confront her hometown and its history, as well as her own history. But she won't do it alone, which is good, because she'll need all the help she can get.

Series starts with Foal of the Forest.
Now with a TV Tropes page.

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.

This story is a sequel to Too Shy for a Rainbow

If you liked this fic, check out the awesome Audio Dub version of it by The Lost Narrator!:
https://www.youtube.com/playlist?list=PLnqCBZacYIwK0xcHv85Lke-xFf5V9p7R4

It's been a month since Fluttershy and Rainbow Dash started dating. Everything was going fine until Fluttershy started experiencing horrific nightmares that started keeping her up at night. Looking for answers, Rainbow Dash, Fluttershy and Pinkie Pie seek out Twilight. But when the three mares find themselves within the world of Silent Ponyville, will things turn out for the better? Or will things end in tragedy?

Sequel: http://www.fimfiction.net/story/14866/Silent-Ponyville%3A-Reunion

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

Two years after Nyx was stripped of the Nightmare's power, Twilight Sparkle is attempting to raise Nyx as a normal filly. But as Nyx's magical abilities begin to grow out of her control, the pair quickly earn the attention and ire of some powerful ponies who do not have Nyx's best interests in-mind.

During the night, the Elements of Harmony mysteriously vanish, and Princess Celestia enlists the aid of their bearers to find them. Twilight is forced to choose between her duties to her princess and her duties to her daughter. In the process, she discovers a web of conspiracy surrounding her daughter that reaches back a thousand years into Equestrian history. Will Twilight be prepared to face the things she learns along her journey's path: about Nyx, about Celestia, about Equestria, about the Elements...

...about herself?

Based on Past Sins by Pen Stroke Pony.
Alternate universe, because Twilight never became an alicorn or princess in this story.