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...

Pinwheel is a simple earth pony. She lives in a little cottage outside Sweet Apple Acres, she makes pinwheels for a living, and she has plenty of friends. But one day, when she goes flying with her good pegasus pal Dizzy, she takes a fall and lands in the dark crossroads between life and death! If that's not bad enough, the Grim Reaper is forcing her to bargain for her life! And what will she do when that bargain takes a somewhat more...personal turn?

Twilight and her five friends are transported during a botched spell, across dimensions to... Ponyville, Equestria? But not the same one that they knew. Sitting on a bench is Harpsy and Babar. The Doctoress avoids apples from an aspiring Applebuck. And in a library across town, six stallions join their forces as they try to decipher the appearance of filly look-alikes of themselves around Ponyville!

The world is a strange and wonderful place, particularly if you are a child of Ponyville. Pound and Pumpkin Cake explore their tiny corner of Equestria.

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

==Originally written spring 2011== Equestria Daily Post==
GLaDOS is free of Chell, free to continue testing, when she discovers a portal gun Wheatley tried to repair with duct tape. When the portal gun catastrophically fails, the enrichment center, GLaDOS, and Chell are literally dropped in the middle of Equestria. The mute test subject soon finds the world of ponies far more welcoming than the human world. But GLaDOS sees possibilities. Let the testing begin... for science.