An accident in the lab sends our favorite boy genius to Equestria, as a pony. What will he do and how will he get back? The answer: Science! (Cover Art Updated!)
New FAQ! and TV Tropes!
Planned Phrases from Dexter:
“Pinkie Pie! Don’t push that Button!” /to Pinkie
“Please, Magic is the word simpletons and the ignorant use to describe what they cannot understand.”/ to Twilight
“No, I didn't strap a rocket to you. I strapped you to a rocket.” /to Rainbow Dash
“Friends? Who needs friends?”

Dexter is a boy super-genius with a disdain for anything girlish and no desire for friendship. After an mishap in his lab, he gets stuck in Equestria. How will he cope with the over-friendly ponies, and the girlish everything?
For any who do not know Dexter's Lab: http://en.wikipedia.org/wiki/Dexter's_Laboratory
[RIP Christine Cavanaugh: 8/16/63-12/22/2014] - Dexter's Original Voice Actress

After the Friendship Games, Sunset feels it's time to return home.

Only when she gets there, Twilight's castle is nowhere to be found, Cadance just got her horn, and Princess Celestia is still calling the bacon-haired pony her prized student rather than a failed one. And just reliving her past isn't on the table thanks to a pair of wings Sunset seems to have sprouted upon her return to Equestria.

With Sunset being back before she's supposed to, will the world stay as harmonious and on track, or will everything go down in flames as Sunset has to deal with allegations that she's really a changeling in disguise, a nerdy stallion with blue hair that wants to be her coltfriend, a pretty pink princess in need of remedial magic lessons, and an annoying purple pre-teen pony that will absolutely not go to bed without first being read Starswirl's Complete Mystical Mysteries Compendium?

Only time will tell

This story is a sequel to The Moon, The Flower, And The Door

Effective Immediately, This Story Has Been Cancelled.

"Anyone Can Be A Wizard..."

Morning Glory has succeeded in passing Princess Luna's test, and is now her personal protege... and soon to be her foster daughter. All seems to be sunshine, lollipops, and fluffy puppies forever... until Luna makes a discovery regarding the young filly's parentage, one that could wound the young filly's heart terribly. Keeping this information a secret seems wisest, especially given the connection the young filly has with Celestia's new student, but it soon becomes clear that this is just the tip of the iceberg, as the filly begins exhibiting strange and seemingly inexplicable talents. The young filly seems intent upon becoming a wizard, in spite of being an earth pony. Is such a thing possible, and is Equestria ready for it? And if so, what kind of a wizard would she be?

One thing soon becomes clear: No matter what the outcome turns out to be, something big is about to happen in Equestria, and when it's all over, nothing may ever be the same....

When Twilight Sparkle was just a kid, her best friend was a girl named Sunset Shimmer. Though their friendship had a bit of a rocky start, they quickly became inseparable, no matter how much everyone thought of them as ‘weird’. They were there for each other.

Were.

Years after the tragic accident that tore them apart, Twilight is determined to move on from her loss, and she sets off on an independent research project to investigate the strange happenings at Canterlot High. Little does she know that she will soon come face to face with what appears to be a literal ghost from her past.

Coverart by Kare-Valgon. Chapter illustrations by Zorbitas.

Edited and Pre-read by Dubs Rewatcher, r5h, and Kalan.

Takes place after Rainbow Rocks, but was written before Friendship Games and does not take it into account.

Chinese translation

Print copies now available.

This story is a sequel to Split Second

Twelve years ago, she broke time. Two alternate timelines exist, each with a different version of Twilight Sparkle. Both versions of her are able to see the other. In this timeline, Sparkle is a Necromancer.

Or rather, she was. Sparkle is dead now, not that she cares. She's got a new body. With Thorn (her undead dragon son) and Cobalt (her apprentice and an assassin for hire) at her side, she's ready to take on the world. Again.

(Spoilers in the comments. Read at your own risk.)

Featured on EQD.
The Tv Tropes page
The Ask Blog

This story is a sequel to Split Second and won't make sense without it.
This story also loosely shares continuity with Lupine Tree. Reading that is not required.

Cover art by Swirling Line.

Twilight Sparkle broke time when she got her cutie mark. Now Twilight and Sparkle are sisters from another time. Twilight is hailed as the potentially greatest light magician of all time, and already has a reputation as a hero by the time she goes to Ponyville. This isn't her story, not primarily.

Sparkle is an orphan - her dark magic killed her parents. She lives with her brother in Canterlot's industrial sector because they can't afford anything better. She can't leave either. She's a natural dark mage; while Sparkle won't go mad like Sombra, her reputation is hardly any better. Worse, the law doesn't see her as a good pony.

The fact that the dead don't stay dead around her, or that Thorn - Spike's double - is an undead, soul-eating abomination, are other matters altogether.

(Also has some Slice-of-Life, but fimfiction tags won't let me put it with Adventure.)

Has an ask blog to go with it: Ask Sparkle and Thorn.
Also has a TvTropes page: Split Second Tropes.

Featured on EQD.

Cover art by Swirling Line.

When Gaberdine is awarded a noble title by Princess Celestia, he soon finds out that his new lands contain several surprises. For starters, there is no land in his new barony. Secondly, his new castle turns out to be a broken-down riverboat. And third is… seaponies.

Baron Gaberdine has a lot to learn about his new barony. And himself.

Fortunately, he has a very young teacher.

Now with a sea-quill (sorry) Drifting Down the Lazy River

Cover photo by PhoenixSwift
Editing/Pre-Reading assistance by Tek, Shaleclaw, Peter, Seether00, Monsieur Connoisseur, GhostOfHeraclitus, The Masked Ferret, Blue Paladin42 and Admiral Biscuit

Note: Unlike The Traveling Tutor and the Librarian, this is a single POV love story, like Changelings, Love and Lollipops. Only with fewer cannons and fountains.
Now Featured on Equestria Daily
With a YouTube Reading of the first chapter by BigAsh
And with a dramatic reading by Neighrator Pony and company Full playlist here.
Thanks for a wonderful review by Paul Asaran
Available in paperback through Lulu.com at cost.

This story is a sequel to The Freeport Venture

Sunset Shimmer has established a good life for herself in Freeport. Sure, the city might be horrendously corrupt, but she makes a very good living as the Freeport's only officially sanctioned unicorn magus.

All that goes down the drain when somepony robs the richest bank in Freeport. And most baffling of all, after the heist the crook went to the poorest part of town and scattered the loot for all of Freeport's poor and deprived citizens. Now Sunset has to find the thief, and figure just why someone would rob from the rich and give to the poor...

Reading The Freeport Venture is not necessary to follow this story's plot, though you'll certainly enjoy it more if you have. Plus you should read the previous story anyway, because I'm quite proud of it.

This story is a sequel to A Moment in the Sun

Sunset Shimmer is on the run. It's been six months since she left her life as Princess Celestia's student behind, but she can't escape her own past. Her parents are offering a reward for her safe return home, and Celestia's agents are watching her every step. She might have gotten out of Canterlot, but the runaway student is still a long way from freedom. Especially since her education with the Princess of Equestria didn’t cover things like how to make a living wage with her magical skills.

However, there might still be one place where she can escape all of them. The infamous island nation of Freeport has long had a reputation as a haven for pirates, criminals, and exiles, but there's no better place in the world for somepony who wants to disappear. The only question is whether Sunset will live long enough to pull it off.

As the eternal regent of Equestria, Princess Celestia's knowledge of magic is without equal. Over her long life, only a few gifted ponies who had a great destiny before them have had the honor of learning at her side. Sunset Shimmer was one such pony: one of Celestia’s best and most promising students. As she learned at Celestia’s hooves, their bond strengthened until they became far more than student and teacher to one another.

Sometimes those closest to us are the ones who can hurt us the most.

[Note: This story does not directly tie into Equestria Girls]