In every event, there are a million offshoots and effects, none really able to be fit into a normal narrative. Here is a collection of one-shots and mini-arcs spun out of The Elements of Harmony and the Savior of Worlds, so knowledge of that series will help immensely. Although I will do my best to make it as accessible as possible.

NOTE!:
All side-stories so far take place after the end of The Elements of Harmony and the Savior of Worlds.
The cast will be varied, as will be the stories, but all are canon.

Chapter One: A Picnic by the Lake: Celestia, Luna and Twilight entertain a guest who is more than meets the eye.
Chapter Two: Time Enough for All: The Doctor has spent nearly nine hundred years in Equestria, most it an extended vacation. But news of giants in Ponyville draw him out of semi-retirement.
Chapter Three: Contact Part One: Old Memories: Chip delivers the Princess' message to President Abernathy, which stirs old memories.
Chapter Four: Contact Part Two: Meetings and Greetings: Equestria makes formal contact with Earth, and an old mystery is finally put to rest.
Chapter Five: Family reunion Part One: The Best of intentions: Dinky sets out to reunite her father with his closest friends, roping her sister and the rest of the Cutie Mark Crusaders on a journey across time and space.
Chapter Six: Family Reunion Part Two: Memories: The TARDIS arrives at Earth, reuniting the Doctor with his past.
Chapter Seven: Shape up or Slaughter Out!: Shining Armor gets some help from an old warhorse to finish what he started with the Royal Guard.
Chapter Eight: How Christmas was Saved... Sort of: A short tale of how Santa Claus was saved one Christmas Or Megan had too much eggnog.

Trope page for The Elements of Harmony and the Savior of Worlds. Story listed there as well.

Equestria Daily page: A man can dream...

Megan Richards is a normal, everyday wife and published author of 'My Little Horsey'... however the tales she writes about aren't fiction, but stories from her past. She thought she put the world of ponies behind her, but sometimes the past has a habit of catching up with you...

G1 meets G4 in a hopefully epic tale of the past, the present and the future.

I own nothing, also, minor cameos from other Hasbro properties such as Jem and the Holograms, Transformers G1 and GI Joe.

Cover image made by the very talented Egophiliac and from here.

fanfiction.net link!
Equestria Daily link... one of these days.
TV Tropes page
All the Tropes page

Sequel: The Conversion Bureau: United We Stand

Side-stories and mini-arcs not able to fit into the main narrative: Side Stories of First Contact

Bon Bon's voice is funny, and that's about all that anypony who meets her notices, as her marefriend Lyra soon steals the spotlight with her explosive personality, strange obsessions, and curious beliefs. And why not? Bon Bon is, after all, a perfectly ordinary, boring pony in every way but two: her voice, and the carefully kept secret that she isn't really a pony.

(Edit:) Now with an annotated version, courtesy of the incomparable Shoggoth Lord!

We all wear a mask called composure, beneath which hides a heart that twists with guilt and hidden feelings. Regal as she is, Princess Celestia is no exception. What might be revealed should circumstances cause this mask to slip - or break?

Set several years after the potential conclusion to the series.

Commander James Bond was one of MI6's top operatives. Having succeeded in countless missions and bringing down international terrorists such as Le Chiffre and Dominic Greene, Bond is sent to Istanbul to retrieve a hard drive containing the names of every agent involved in undercover affairs. The hard drive in question has fallen into enemy hands, and it's his job to get it back.

After disastrous events in Istanbul during the mission, James finds himself in an unfamiliar land, and soon becomes entangled in a tale of international espionage.

Only one man can protect Equestria and its princesses in this new time of crisis, and his name's Bond.

James Bond.

A sequel has been published: An Equestrian Princess in London.

The alicorns have been struck by a fatal illness, and Twilight and her friends must find the cure: a panacea hidden in the deepest reaches of Tartarus. But Tartarus is unnavigable to those who cannot withstand the chaos in its depths, and the spirits of harmony are no exception. To obtain this cure, Twilight and company will need to find ponies who can traverse Tartarus, a task that will take them to the edge of the world and back. Supposedly, these ponies have two things in common: they've all crossed paths with the mane six, and none of them ever learn from their mistakes.

Inspired by, but not quite based on, Braid.

AU tag for deviation from Season 3 canon.

((NOTE: "Twilight's Kingdom", all information revealed in it, and all events after it are non-canonical to this story.))

When strange black clouds gather over Equestria, it marks the beginning of a dangerous new adventure. Now the Mane Six must travel to a strange, dark realm to save the friends who are being held prisoner there. Will they succeed? Or will the darkness of this world consume all of Equestria?

Based on the original My Little Pony TV Special, "The Rescue from Midnight Castle".

Cover image by the highly-talented Elisto from deviantART: www.elisto.deviantart.com

Applejack's got a secret she'd kept hidden for many years. Nopony would ever have guessed what she and Twilight were up to in the library late at night, once Spike had gone to sleep. That is, until a jealous Rainbow Dash decided it was her business to find out just what in the hay was going on.

Twilight Sparkle just can't find enough time in the day. She has to study friendship for the Princess, hang out with her five friends, and juggle her own hobbies and interests besides. But when a novel solution presents itself in the form of an experimental new spell, will it solve her time crunch, or will she be distracted even further?

Pinkie Pie is haunted by feelings of self-hatred, stemming from the day she left her family to be on her own. Never wanting to see her best friend in a crazed state of distress again, Rainbow Dash resolves to reconnect her with her estranged family and bring an end to the personal demons once and for all.

Featured at Equestria Daily on September 28, 2011.
Featured at Canterlot's Finest on November 21, 2013.