Originally Posted by
Viridian
Double Fault and Recombinant are definitely my two favourite pieces of PoT fanfiction as well. I wish there were more good non-shounen-ai (or at least, very well written ones) stories, and I'd appreciate it if people could keep offering recommendations.
As for my own recommendations, I'd like to mention "Kittens" by dyaoka. Unfortunately, the author hasn't updated in years, but it is still a good read. Oh, and it's also AU.
There's also a one-shot that I rather like (although there may be mild shounen-ai hints, but it definitely falls under the "very well-written" category): Canon by Lady Androgene.
EDIT: I forgot about a complete story by dyaoka, called "Darkness Falls". That's also a great story, albeit quite creepy.