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.

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

During a blissfully rare calm in the hectic storm of Ponyville life, a disturbance in the Everfree Forest goes undetected. After receiving a summons from the Princess, Twilight and her friends are led into a curious task, one that they find themselves ill-prepared to handle - managing their stallion double! As each of the girls meets their very own carbon-copy-colt, they learn that dealing with themselves can be much more frustrating than they first thought.

Annoyingly, irritatingly, intoxicatingly frustrating.

http://www.equestriadaily.com/2011/10/story-giving-love-helping-hoof.html

She was his first friend, his dearest friend, his oldest friend, but after all these years he has to let her go. He doesn't want to, but sometimes you don't get your way. Goodbye Fluttershy.

After Pinkie Pie Suffers a severe head injury, in her forehead is discovered something that an Earth Pony should not have. This gives answers to where she gets her abilities, especially how she seems to be able to defy the laws of physics. This also explains some of her craziness.

How will her friends handle this, and can she learn to better harness the magic within?

A big shoutout to Aegis Shield for the original idea. I would not have thought of this one myself. You, good Sir, are brilliant!

Cover image by sapoltop on Deviantart. I lay no claim to the artwork. The artwork is his creation.

A thousand of years of life experience would no doubt teach Princess Celestia much about romantic relationships, and that is exactly what Twilight wishes to learn from her beloved mentor. When Princess Luna catches wind of these lessons, however, she sees a chance to relight the fires of love within her sister again. But when a “one-time fling” turns into a life-long infatuation, Luna and a reluctant Cadance must race to reverse the effects of their meddling before Twilight finds herself in a most compromising position!

But can she truly resist the total affection of a goddess?

Title says it all. Time travelling shenanigans ensue.

Twilight wakes up and finds out that she's changed back into a filly! What kind of trouble will she get into? How will her friends react?

(Second Person fanfic)

You have just moved into your new apartment and look forward to your new job at a bakery. You think life could not be any better, that is until you meet your neighbor who looks and acts like Pinkie Pie. Will you get along with this hyperactive funny girl, or will she drive you insane?

It was the happiest I had been my entire life.
I was able to forget and move on. For the rest of my adolescent years I lived out my life in a satisfied stupor; careless to the rest of the world and only focusing on my friends and my job—most of the time. For three years I lived content and lazy in the beautiful town of Ponyville. I didn't expect that my life would be so full of adventure and fame. I only expected to escape my old life, but instead found something even more grand and beautiful than a mere vacation from my suffering.
I wanted more than anything to keep it from all falling apart.