I must confess, the thought of reading fan fiction has always been difficult for me.  However, I have known about many very well received fan fictions in the brony fandom even since my early days of joining the herd.  And the one story that has been recommended to me more than any other is Past Sins by Pen Stroke.

Check out the story here:
http://www.fimfiction.net/story/41596/past-sins

DRWolf Images by CiderSplice:
http://www.deviantart.com/art/DRWolf-Avatar-Confused-395260247

My Little Pony Characters and Images belong to Hasbro.