Part of the fun of owning a website is being allowed to promote whatever you want. The links below are great and were definitely worth my time, so I hope you will enjoy them.
The technological singularity, through friendship and ponies. The writing isn't fantastic, but the ideas behind it are brilliant. This literally inspired me to change my life.
A story set in the same universe as Friendship is Optimal. The writing is better, and it focuses much more on the existential crises of uploading. It terrified the hell out of me.
It originated as a Flutterrape story (a very specific genre of story from the depths of 4chan, where all the ponies want to sleep with the only human in Equestria), but it turns into an epic romance adventure where the main character falls in love with the Best Pony. The fact that there is no sex only makes it better, in my opinion.
Be warned: This story is dangerous for your mental health. The main character is kidnapped and turned into a pony, and then brainwashed into a pet. It really goes into the psychological aspect of the transformation, which is terrifying and hot at the same time. Be warned, lots of sex.
Von Kreiger writes a lot of great herm transformation stories (or used to) and this one is by far my favorite. It's straight porn, but good stuff.