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 Vanilla Twilight

Rainbow Dash has a problem.

She might be in love with Twilight Sparkle and has yet to admit it to anypony, least of all Twilight herself. After the events of Vanilla Twilight, the two have grown much closer together, spending more time together and sharing their interests. Unfortunately for Dash, Twilight hasn't caught on to her feelings yet, and she could be content with just letting things progress as they are...

If only she hadn't sent that blasted letter admitting it.

Now, thanks to a pair of meddling princesses, Rainbow Dash finds herself on a globe-trotting journey with the subject of her affections. On the surface, it might just seem like a simple task for the Princess, but for Rainbow Dash, it might be the very thing that forces her to come clean with her feelings, or forever face her doubts. For her, in the world of life and love, sometimes it's best to take it one dream and disaster at a time.

This story is a sequel to The Code's Apprentice

Sequel To : The Code's Apprentice

The land of Equestria has been changed forever.

New monarchs sit upon the thrones of the Sun and Moon, the once almighty power of Harmony overturned to make way for a new Diarchy of Balance. Political unrest and turmoil have engulfed the land, and at the very center of it all, Princess Celestia - renamed Tia Sunbeam - seeks atonement for the crimes she committed in the name of Eternal Harmony.

With much of her power sealed away, Tia must live amidst the citizens of Ponyville as the world changes all around them. As Ponyville works to rebuild following the struggle between student and teacher, they must cope with the edicts of a new government determined to bring equality to all creatures, beliefs, and ways of life - even those that were long since banished to the dark places of the world.

Tia Sunbeam will struggle with her own deeply held convictions on the way the world should be, versus the way it will now become. She will face a truth she has long since denied, and realize the true meaning of Harmony. And perhaps, most importantly of all... She must make some Friends.

Cover art by SinSays at http://sinsays.tumblr.com/ - Go spend some money with her! :D
Oh, and go check out my new side story - Rise - It's going to become relevant here!
(character tags are not comprehensive! Some are being kept secret! ;3)

This story is a sequel to Fashion Crush

(Humanized) Vincenza Scratch, AkA Vinyl for her friends, AKA DJ-PON3 on stage, 22 years old. The DJ found herself in one of the low periods of her young career, probably the lowest and longest she ever experienced so far; writer's block, out of ideas for a new genre of music as her 'classic' electronica seems to go out of the crowd fashion, less and less attendance to her gigs, etc.

Starting to run low on money, She gets in touch with one of her mother's friend in the capital, Vito Philharmonica; Member of the board of one of the most prestigious private high school. Vito offers her a place to stay and a job to help her to get back on track : A music teacher job for a Highschool senior class, which includes Vito's own daughter, Octavia.

How's Vinyl going to teach to a bunch of teenagers when she's barely older than them? ( and probably not much more mature as well). And when other teachers and some of her students look down at her for being a 'simple' DJ? One answer, Becoming the GTVS: THE GREAT TEACHER VINYL SCRATCH! (Yes inspired by GTO, one of the coolest manga ever)

Fanart for the story on tumblr or on DA!

Don't forget to check the comic version as well

This story is a sequel to The Golden Armor

It's more of a continuation than a sequel, but whatever.

Comet is the leader of Princess Celestia's personal guard. Angel is the leader of Princess Luna's.

Comet is awake during the day. Angel stays up all night.

Comet likes using a halberd. Angel excels at using claws.

Comet is a pegasus. Angel is a bat pony.

Together, they take on all the twists and turns life hands them. However, things don't always go as planned.

Cover art by Equestria Prevails.
Proofread by jmartkdr and Feather Scratch

"... at the forefront of our fandom’s writing scene ... Masterpiece." —PCaRG
"... really enjoyable ..." —City of Doors
"...worthy of high praise." —PaulAsaran
"Lots of wonderful world-building, great action, well-developed characters and an engaging story." —Hoopy McGee

Steel Song is a lot of things. Earth pony. Uncle. Professional bodyguard.

Retired.

So when he receives a mysterious package from Princess Luna a few weeks after the changeling invasion, he's understandably apprehensive. More-so when he presents himself before the Royal Diarchs to find that not only do they desire him to come out of retirement, but to take command of a most unusual position...

A position that may have more significance than any of them suspect. Because strange thefts are occurring on the Equestrian Railway, thefts that nopony can explain. Thefts that may have far more sinister intentions than their seemingly innocent nature may convey.

Intentions sinister enough to shift the balance of power in Equestria forever.

Book I of The Dusk Guard Saga.
Epic Fantasy
Has a collection of Side Stories as well, the first of which is here.
Now with a TV Tropes page!
"This is 100% Approved by Twilight's Library!"
Added to Twilight's Library 11/26/2013
Added to Canterlot's Finest 12/01/2013

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)

It's been ten years since Rainbow Dash's father disappeared in a wild, fierce thunderstorm. When the same strange storm hits Ponyville, Rainbow Dash does as much as she can to try and stop it from happening again.

But magic has a strange habit of making things reappear, opening old wounds that could change Rainbow Dash's life forever.

This is a fic based on the Time Loop Files, the format of which was first codified by Innortal on fanfiction.net.
Here's a brief guide.
The basic idea is, one character (the Anchor, usually the main character of a fictional setting) is looping back to the very first moments of their parent series every time either they die or some kind of time limit expires. They of course end up monumentally stir crazy given enough time.
Eventually others start to loop as well.
The reset is not always perfect. Sometimes a loop's history will be different to the "prime" loop, or canonical plot.
"Crossover" or "Fusion" loops also occur, randomly. These can involve the home loopers having a guest, or the anchor for one universe spending time in another, or replacements of one character by another.
Vacation Loops are where the Anchor (or others) decide/s "buck it" and lets off steam by doing whatever comes to mind. There's little or no attempt to maintain the original timeline.

In addition, and particularly more recently, it should be known that this story has a collaborative element to it - people may submit loop ideas or loops, ideally at the Spacebattles thread (a link to the current version of which is on the Trope page), and they may become included.

There's two page image options, thanks to Filraen - the current page image has been edited by the original creator from this work of theirs.. The other one is here:
http://hourglass-vectors.deviantart.com/art/MLP-Loops-466030169