Good fan fiction isn't found easily. However, Shamus Young wrote an on-line novel, titled Free Radical, which is an excellent adaption of the System Shock storyline.
Some qualities of the novel include in-depth knowledge about artificial intelligence, encryption and hacking - topics which the author lectures with an authority and passion not quite unlike the kind you would expect from books by Neal Stephenson. The novel manages a fine balance between the intellectual, claustrophobia and action. It covers most of the topics we've come to expect from cyberpunk, like evil corporations, street ninja and cyberspace.
It can be found on www.shamusyoung.com