A few more I have found after going on a bit of a Gunslinger Girl kick
GSG Great EscapeSet just after season two of the anime, and throwing out the manga past that point. Quite a few gramatical errors, but it stays more or less true to the spirit of the show. Of course its still a fic about the cyborgs going off the farm and aiming for revenge, but its fun, and updates with decent regularity. (now that I said that it'll probably die, my praise seems to be a curse of some sort)
CoscaThe premise is that the SWA has more cyborgs than they do handlers, and decide to have Triella take a set of twin cyborgs they just finished under her wing. A bit odd as far as premises go, but fun, and well done imho.
One Hell of a RuckusGunslinger Girl, crossed with Black lagoon and Baccano. It follows the Baccano style of one incredibly fucked up event explained in incredible detail, and not only does it involve a decent amount of the Baccano characters, but all of the most loveable degenerates from Black Lagoons take on Roanapur. Of course it starts by explaining how all of hte cyborgs save the only live one died in the meanest ways possible for them, and its dead and unfinished, but whats there is a fun read.
Alternate RewardsGunslinger Girl fluff, but its amusing enough, and decently funny.
Gunslinger Girl: The First PrioritySadly jsut an intro, but funny and believable enough. A shame that it never got off the ground, as it shows promise.
And heres what came of me going on an Eva kick before the GSG kick I'm coming down off of, haha.
Eva: Speak with DeadSupposed to be a rewrite where Shinji was raised by the Hellsing organization, but it died shortly after teh introductory/setup chapters. Still fun enough, all things considered.
Neon Genesis Evangelion: EmpathyNot sure if it has been recommended yet, but I think its one of the better Eva rewrites, and deserves it again if it has been. The premise is a tried one: shinji has a spine and understands others... but its done well enough for that to be something easily looked over. Nearly complete, and not looking like its gonna die any time soon.
Neon Genesis Evangelion: Red Moon RisingA strange premise witha somewhat superpowered Shinji. It gets more than a bit... strange, towards teh end when things go to hell as Eva fics are want to do. Still amusing to read, despite the intense Asuka/Misato bashing at the end.