I maintain a Pony Fanfiction Index on my website. You can find it here. It includes only the fics I think are the best of the best (of the best). It also only includes complete fic. Keep in mind that this list is entirely subjective to my tastes and interests; however, if you need something to read, it's there for your using. I hope you get something out of it!
Things I Draw!
The Enervation Sequence
The Mane Six click into opposites mode, and events compound. The first step of the Enervation Sequence.