The story is generally the same. A group of ponies go on a quest to stop an insane alicorn who had escaped banishment, learning about friendship along the way and mastering the Elements of Harmony. But the details...

It can be Trixie Lulamoon leading the Elements of Harmony against Corona.
Rainbow Dash could be Celestia's student and go to Ponyville.
Equestria could have a deep connection to three young people in its distant past.
The Elements of Harmony could have been moved to Manehattan for the ponies to quest for.
Princess Cadance might rule over an Equestria of music, with Octavia as her prized protege.
Or Spike and Twilight might have their roles reversed, the former a stallion and the Element of Magic.

And each one has been chosen by Discord, an Element removed to a seventh Equestria for purposes as yet unknown. Can they survive? Can they get home? Read and find out!

The Lunaverse was created by RainbowDoubleDash and is used with permission. Opening segment was written by Talon and Thorn.
The Hasbroverse was created by RK_Striker_JK_5 and is used with permission.
The Manehattanverse was created by Little Jackie Papercut and used with permission.
The Cadanceverse was created by GrassAndClouds2 and used with permission.
The Flipverse was created by Bed Head and used with permission.
The Dashverse was created by Trinary and used with permission.

And special thanks to dramatic_spoon for getting this all together.

When Ruby boards the first trans-oceanic flight in Equestrian history, the last place she expects to end up is stranded in the middle of Eternity's Crossing in the wake of a horrific zeppelin crash. After a mysterious tower leads her and a fellow survivor to discover a twisted and fragmented city twenty thousand feet below the surface of the ocean, though, a bit of fire and smoke is the last thing she needs to worry about. Between the horrendously disfigured residents and the paranoia of the madmare who once built and controlled it, daily survival in this corrupted utopia is anything but a guarantee. But with the help of some new friends and a few genetic enhancements, Ruby isn't going down without a fight, and in the process might just discover that the deadliest weapon in Harmony is herself.

An adaptation of BioShock for the world of MLP. Written to be comprehensible to anyone, regardless of whether they've played the original game.

Lunaverse story. A thousand years ago, Corona cursed Jackelope Valley, and it has never rained there since. Now the barren desert is the site of an annual music festival that celebrates up-and-coming artists--and Lyra's been invited to play! When Raindrops learns that her favorite band, the Daughters of Discord, are playing, she comes along as well... but soon after arriving, the two stumble upon the last living Jackelope. What should have been a week of fun and music turns into a race against time and the pitiless sun as the two ponies, aided by DJ Pon3 and the guitarist pegasus Thunder Axe, struggle to save the Jackelope's life...

"OC" to refers to Thunder Axe and assorted background/minor characters.

When the Cutie Mark Crusaders dig up an ancient magical artifact, they unleash a spell on the town that allows everypony to see a "lie meter" floating above each other's heads. While attempting to solve the mystery, Twilight Sparkle has to analyze the tenuous balance between friendship and honesty. She doesn't like what she finds.

Based on a story idea conceived by theworstwriter
Written and posted with his permission

(A collab by JaketheGinger and Luminary)
Equestria isn't what it should be.

Celestia is a figure of distant mythology. Progress has replaced harmony as society's watchword. Progress born of spell, steam and gears. A dark corruption eats away at Canterlot and stretches out its influence.

In the shadow of the dying capital are scattered points of light. The selfless pink toymaker, caring for nothing but a smile. A unicorn noblemare feeding the ghettos. An airship captain who gave up wealth and status to stamp out injustice. They, amongst others, are thrown together by danger and flight, and find themselves gambling on a desperate bid to restore Equestria.

(Welcome to EqD ponies! Thanks for the feature!)

It's been said in prophecies that nopony will know the time or date the magic of Equestria that empowers its citizens would leave. I thought it was just superstitious nonsense written by ancient witch doctors. In a sense, they were right. But I would have never expected it to come like this. —Princess Twilight Sparkle, 05/05/1268

AU tag added due to the Cutie Mark Crusaders getting Cutie Marked.

There is a secret in Equestria. A secret the newly crowned Princess Twilight Sparkle doesn’t dare to believe. Like puppeteers pulling on marionettes, they have influenced Equestria for better and worse since the fall of Discord. So far they have been benevolent, but their potential for evil is vast. What’s worse, she doesn’t know their name. She doesn’t know their mission. All she knows for certain is one thing.

That they all seem to be zebra.

After the Changeling invasion, Celestia and Luna make the decision to have Twilight investigate the Elements of Harmony and solve the mystery of their power.

A thousand years later, Rainbow Dash awakens in a world she does not recognize. She has no idea how or why she came to be there. She does not know the language, the geography or any of the rules of this new time. She soon finds allies in Star Fall, a scholarly pegasus whose Talent is Magic, and Astrid, Star Fall's Griffin guardian. Together they set out to discover why Dash has been sent to the future, and how she might return to when she belongs.

War threatens the nations, a Nightmare stalks the shadows, and Rainbow Dash's arrival has turned her into a wild card in a deadly game that pits the law on both sides of a broken Equestria against a mysterious criminal figure, Max Cash. Yet the stakes are higher than anyone knows, for in her research Twilight Sparkle discovered a dark secret about the Elements, something that will shake the foundations of the world.

Cover image by SierraEx
Has a TvTropes page

Twisted Spare, while studying a book of myths, comes across a terrible prophesy: the ancient evil of Queen Husk, once sealed inside Queen Chrysalis’s heart by the Elements of Unity, is predicted to emerge as a twin to an unloved Goddess—on the date of the coming Change Carnival! Despite her student's worries, the Queen sends Twisted and her assistant, Gaze the cockatrice, out to the hamlet of Fangville, where she is to oversee the preparations of the Carnival.

Where she will meet five certain Changelings that will change her life her forever…

((Cover by Shadowfoxnjp on FA.))

Equestria stands at the dawn of a new golden age of harmony and enlightenment. Six normal ponies have taken up the tools of the gods and defeated the greatest evils of history. A bookish unicorn filly is set to usher in a magical revolution. The first new alicorn in a millennium provides the promise of a coming era of peace and love.

Change is rarely peaceful.

In the wake of the Royal Wedding, the nation struggles with a scattered army which feeds upon the very thing that stands to elevate ponykind. However, Equestria's citizens, her heroes and even her gods discover that it is the enemy within that one really needs to fear.