This is meant to be an exhaustive list - I am going to list literally all the fanfiction there is. Let me know if you've found more I haven't found, or if you'd rather not be linked.
Spoiler warnings apply for all fic.
narugami wrote beautiful end-game fanfiction here. She also wrote an excellent AU here. And a lovely series on Jade, Anise and Florian here.
ranchelle and yukihyou have some excellent stories up here.
fate_repeated wrote Jade/Dist here.
pic_murasaki's Abyss fanfiction is on tales_of_yaoi.
chibimazoku wrote Guy and Luke, young!Luke and Guy, and Asch and Luke: on girlfriends. Really sweet Guy and Luke fic here, with art! All fic here.
Picup wrote a Yuria drabble (midway through page), a Natalia story, and a Guy/Natalia fic. [SO the Abyss fic has been hiding in the Symphonia category!]
Tear and Luke by griffinkhan.
I wrote some here and here.
There is a Tales of the Abyss fanfiction section on aff.net.
There isn't a specific Abyss fanfiction section on ff.net at the moment, but all Abyss fanfiction is going in the Symphonia section for now.