Synopsis: The largest MLP: FiM fansite. In addition to other fanworks on the site, its archive of fanfics can be found here, or if that list hasn't been updated recently, the individual posts for each story can be found here. Every story is reviewed by pre-readers before being posted, so they are at least grammatically competent.
Synopsis: The other MLP fansite. This one focuses solely on fanfiction, and as a pure fanfiction site, has superior tools for finding stories than Equestria Daily... but also has lower standards so Sturgeon's Law applies. The two sites have a fairly close relationship though, so most of the best content is featured on both sites.
Synopsis: A MUSH-type roleplaying environment, based on the series-proper and keeping about as close to canon as one can with roleplay and whilst allowing original characters. Play is centered on Ponyville, but takes place in other areas, also.
Synopsis: An imageboard section dedicated to reviewing and critiquing MLP:FiM fanfiction, particularly prior to an author's submission to fanfiction repositories like Equestria Daily and FIM Fiction. Authors can find dedicated reviewers to help them pre-read and edit their stories, as well as brainstorming and story creation threads. Sites such as Equestria Daily often refer stories which are initially rejected to the reviewers of this community to help them improve the stories prior to re-submission.
Synopsis: A play-by-post RP forum, Equestria Chronicles has a constant continuity and a very friendly community. The story itself is rather grimdark, with Tyrant!Celestia being played absolutely seriously, but it focuses more on individuals and allows for many subplots.
A tumblr blog which posts a prompt every day and gives writers 30 minutes to write a story based on it. The stories can be of any genre, but must be SFW. A very good source of well-written short stories.
Eakin is an action-oriented author best known for the Time Loop Trilogy: Hard Reset (link), A Stitch in Time, and You Can Fight Fate, with a spinoff sequel in the works. The trilogy follows Twilight as she works to stop a series of cascading crises, and is told in a colloquial, direct, and humorous style. All of the characters fit their canon personalities perfectly. It's got elements of everything: philosophy, relationships, absurdity, despair, and Twilight beating up a ton of changelings—definitely worth a read. Eakin has also written a worthy contribution to the Friendship is Optimal universe (link), as well as a number of one-shots and other stories. Just be warned when reading his stories featuing humans however, as they tend to portray a lessthan favorableview of us. The infamous XCOM: Enemy Unthreatening received wide internet flak for his portrayal of humans and the princesses.
Synopsis: This artist/author draws exclusively FiM art and most of it shipping related. There are three stories featuring his couples and their kids currently though one is still unfinished. The stories are very sweet and the fan kids are darling. His pairings are Lyra/Bon Bon, Twiluna, Discord/Celestia, Carameljack, Fluttermac, Braeburn/Pinkie Pie, Soarindash, Sparity, Scootabelle, Doctor Whooves/Derpy, Apple Bloom/OC, Diamond Tiara/Twist (though it's only a background) and several OC/OC pairings. If you have the time to browse, both the stories and artwork are wonderful. However there are some dark elements included in all three stories. The stories are called Tootsie Flute Makes Three, Spike the Werepony and Luna the Matchmaker (currently unfinished).
An author with a rich and elaborate style, The Descendant sets his touching fics in a sort of a serious fantasy version of Equestria. The fics all figure, more or less, into an overarching plot, though each stands on its own as well. His stories are varied (from silly comedy through philosophical musings to dark fantasy), though mostly rather light-hearted (if not shying away from darker and mature topics). One can also spot some Christian philosophy in his fics if one cares to look.
Comments: There are no words for how epic this man's stories are. Seriously, just go read them. You might find VinylScratch, or Surprise, or even The Doctor! But I can guarantee you will find epicness up the a$s!
A real-life high school teacher, he writes Cheerilee with a kind of authenticity that's hard to match, and gives her an endlessly entertaining and quirky personality. His story "School Daze" is a loving tribute to the Stand and Deliver, and even includes multiple song numbers and an honest-to-god Training Montage. He's also a huge Doctor Who fan and has done a great job turning Derpy into a lovable and believable romantic lead for Dr. Whooves. Seriously, he rocks. Go read his stuff.
I've only read a couple of his fics, both comedy (The Many Secret Origins of Scootaloo and The God Squad), but those by themselves give him my recommendation. Both fics are pretty good examples of postmodern absurdism, and you'll probably be laughing your flank off reading them. He also has a few more serious sounding fics (going from the titles & descriptions only that is), one being Film Noir-ish, showing he has range. That said, the fact that the first mentioned comedy fic has it's own tvtropes page should say something.
Mind you, that marijuana scene with Rarity and Fluttershy getting stoned? Also a heartwarming examination of introversion (Fluttershy) and extroversion (Rarity), with both parties comforting the other that there's nothing wrong with the way they behave.
Want to read a shipfic starring everyone's favorite number one assistant?, this is where to go! Mallajong 1 specializes in ship fics starring Spike, and he writes them quite well, with said fics actually feeling like legitimate blossoming romances for Twilight's surrogate brother. Highly recommended, please support his goal of getting Spike all the bitches.
If you're a fan of Star Wars, then you should love Doc Delray's Star Wars/MLP crossover Of War and Friendship, and its pseudo-sequel On the side. "Of War and Friendship" and "On the side" are stories about a merging between the Star Wars and MLP universes, and features a great many mythological reasons to explain this merge. This, coupled with a fantastic story, great original characters, and interesting interpretations of existing ones, makes Doc Delray's works some of the best I've ever read.
Tragicom recently started a series of Doctor WhoFusion Fics based on classic serials. So far, these have included adaptations of:
The FiveDoctors - Bon Bon as Tegan (Word of God is that Lyra will be Nyssa if she ever appears in a story), Caramel as Turlough, Shining Armor as the Brigadier, Twilight as Sarah Jane, Colgate as Romana, Derpy as Jo and Private Pansy as Jamie.
"Just a humble writer with some stories to tell"- but what stories! Author of a series of (mostly) one-shots delving into the backstories and relationships of the Mane 6 and CMC, amongst others. Not only do they serve as a frequently heartwarming (and occasionally tear-jerking) look at the ponies we know and love, but they gradually introduce choices and connections that steadily hint at both a dark past and a dark future for Equestria. "Each story, each secret, each moment brings you ever closer... a storm is coming."
If you want an expanded look at the Equestria Girls world, this is the place to find it. Jay has an entire continuity of stories set in the world, and everyone gets a little bit of love, but special mention has to be given to his take on the Sirens. The first story can be found here, while the list of stories in order can be found here. Also keep a lookout for his Night and Day storyline.
A very underrated writer with an interesting catalogue of works, ranging from adventure to horror to propaganda to christmas-special! If you're looking for something with an epic, adventurous high-fantasy sort of feel to it, then look no further than Redback's fic, The Tears of Gaia. It's currently ongoing, but it is beautifully written, rife with scenery porn, magic and even song numbers! And if adventure isn't your thing, he has also written very many Lovecraftian horror fics, including straight adaptations of Lovecraft stories, such as The Statement of Twilight Sparkle, The Strange Music of Octavia, and Scaling the Tower. He really has the Lovecraftian style of atmosphere and chills down pat.
And his latest project, Kingdom Come, looks to be on its way to becoming something huge. Another darker fantasy story, it is apparently set have multiple tie-in sidestories and possibly even a prequel! definitely worth keeping an eye on.
A Fimfiction.Net author of three novels (two complete, one incomplete, about ChangelingInfiltrators. They are notable for their excellent characterization and in particular well-paced, well-plotted examinations of Becoming the Mask. In "Without A Hive," Nictis (a young Infiltrator) is stranded among Ponies and forced to maintain a Pony identity for a very long time (trope entry here); in "Fragments," we see some of the aftermath of the Battle of Canterlot from "A Canterlot Wedding." The still-incomplete "A New Way" is a sequel to both earlier books.
MLP Collateral Damage - Falcon Punch carries a vital package from Appleloosa to Canterlot; the elite Changeling Infiltrator Ceymi is ordered to kill him and take the package. Takes place YOH 1481, 19 years before the Return of Luna.
"Ruminations In Stone" - Trapped inside Discord's stone statue, Wind Whistler considers her situation.
Nightmares Are Tragic - "The Elements of Harmony" from Luna's perspective. Explains exactly why Nightmare Moon seemed unusually easy to defeat. Takes place June 21st-22nd, YOH 1500.
An Extended Performance - The Great and Powerful Trixie finds herself fighting an evil cult in Manehattan on the day of Nightmare Moon's return.
A Long Night At The Hippodrome - Baltimare theatre impresario Piercing Gaze faces the Longest Night in Equestria. Side-story to An Extended Performance.
His Mark On History - First Strong Messenger strives to strike a blow for his country's freedom from the Griffon Empire by assassinating the heir to th ethrone and make his mark on history. Mostly takes place June 28th, YOH 1500.
All The Way Back - The emotionally damaged and weakened Princess Luna slowly recovers her sanity and power.
Divine Jealousy And The Voice Of Reason - Late Season 4, 4 years after Luna's Return. Fluttershy's in love with Bulk Biceps, so Discord consults his inner Voice of Reason to decide what to do about the situation. The Mane Six, the Pie Family and Princess Luna also get involved.
Fools And Drunks - Early Season 5. Snips takes Snails drinking in the Everfree Forest to celebrate Snails' 16th birthday, and the two lads run afoul of the Wraiths of Sunney Towne.
The Fall Of Hive Hunger Prime - 15 years after Luna's Return. The Great Changeling War enters its last days, as Equestria prepares to smash the last of High Queen Nightmare Hunger's Hives: Theoretical Infiltrator Compound and her two buddies Carry and Cowl struggle to survive amidst the madness.
Twelfth Equestriad Interview - 48 years (12 Equestriads) after Luna's Return, and 24 years after the final victory over the Shadows, a talk show host interviews Princesses Luna and Twilight Sparkle.
One of the best authors on Fimfiction.Net. Often writes stories that are darker and more serious then normal, but still manages to keep the tone of the show. Always writes characters well. (especially Rainbow Dash)
Member of Fimfiction.Net since September 9th, 2013. Justice is a master at writing bizarro comedy and parody, and most stories intentionally flanderize certain characters for the sake of humor. He's also responsible for the story The SweetieMash Chronicles. Other stories I'd recommend are:
Member of Fimfiction.Net since March 1st, 2012. Merc possesses a relative simple writing style and stories that emphasize action and deep emotions. He usually won't make you think too hard, but you'll be too busy laughing, crying, or cheering the protagonist on while she beats the villain into pulp to care. Watch for language and mature themes, not to mention the majority of his work is purely Humanized and AU, but an excellent grasp on the core characters (plus a great sense of worldbuilding) makes his work worth the time of any fan.
Best works include:
The Laughing Shadow. Merc's crowning jewel, this story has it all. A Rari/Jack Romance (with a NSFW optional sex scene); a splendidly built AU; tons of movie action, complete with swearing and violence a-plenty. Sequel coming!
Fool's Gold. Actually the first story in the collaborative Heistverse, written with JaketheGinger and Peregrine Caged. This is another Humanized AU, filled with violence and mature themes as the girls rob a bank to stop an evil tyrant.
The sequel: Diamond in the Rough Still full of action, but with much more world building and character play to expand the groundwork from Fool's Gold.
Side Stories: Big Red and Colder Weather take place during the primary Heistverse stories, but expand on either fewer characters in between or other characters in the world.
Both Outpoint and Dust on the Bottle update infrequently and aren't quite as strong as his main stories, but are still solid Humanized AU that really explore the characters and various relationships between them.