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First, there is the System Shock Hack Project, an unfinished reverse-engineering of System Shock's engine.
They've been working on it since 2001, and I think the last update was 2008. It's very counterintuitive to work with, and I still don't know how to decipher it. I'm impressed with what was done so far (based upon screenshots), but I don't know how to get this working right. Especially when the latest release doesn't have a readme or the files on what to do.
Secondly, there's Revert3D.
This is incomplete, too. However, it's got a nice little tech demo to go along with it, and plays very nicely. Especially when you grab boxes and stack them to get to a difficult to reach area (a la Deus Ex). I don't know how to work around this engine either, especially when I was trying the editor. I'd like to see what this engine could do, but it seems like it's been halted due to whatever's going on in the creator's life.
And finally, there is this:
This guy's managed to make enormous progress for a remake of System Shock on Unity, and it's open source.
I'm looking really forward to this project getting finished, and it might be what I'm looking for. Interestingly, the creator originally was doing this for Dark Places, but switched engines out of the need for more flexibility (and for more volunteers). It's showing more progress than the Citadel Conversion Project on TTLG Forums, which hasn't had an update for three years.
Anyway, I just thought these links would be of interest to my creative brethren.