Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

While at a slumber party telling spooky stories, Twilight learns of one story that is supposedly true, and just has to investigate...

(Featured on EqD.)

(Audio version by Thornquill.)

Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

This is a realistic view on how shipping would actually happen in the show. Almost every pony has been shipped with everypony else, but this is what would actually happen if two ponies ever attempted at a relationship.

...

No offense to any shippers, even though you shouldn't take any. If anypony would like to see any other shippings done on this fic, just leave a comment. Maybe I'll write it if I feel like it.

When Ditzy Doo loses her job at Cloudsdale Mail and Freight, she gets a job at another shipping company... only to find out their definition of shipping has nothing to do with delivering packages! Desperate for income to support herself and Dinky, will Ditzy be able to make it as a pony matchmaker?

(Occurs between Seasons 2 and 3 of the show.)

Twilight is an intelligent mare, and always has something to say. But when a group of bizarre creatures shows up at her library offering life long service and devotion, for once she's at a loss for words. Which is too bad, because she'd really love to ask: what's a human and why are they so weird?

Story Image by: Megan Lara

The Ponyspawn have invaded Equestria, and it is up to the newest addition to the Grey Wardens, Twilight Sparkle, to find the means to drive them back! With her friends and allies at her side, can Twilight defeat the evil tide before all of Equestria is devoured?

The Sequel, Pony Age: Catalyst, is available.

Rainbow Dash finally did it! A sonic rainboom on command! Except she also managed to break every window in Applejack's farmhouse in the process. Now she has to pay for each one, and with her wages from managing the weather not nearly enough to cover the damage, she has to work on Applejack's farm for two whole weeks!
Talk about cruel and unusual punishment. Still, maybe it wouldn't be all bad. At least she would get to hang out with her friend AJ right? Wrong.

5-star featured on Equestria Daily.

Sequel: http://www.fimfiction.net/story/4620/Breaking-Barriers