Re: Dark sci fi games.
Never heard of 'Singularity' and 'I have No Mouth And I Must Scream'. Good call on the Quake games, brings back memories. (dat Trent Reznor collab!)
Some other good cyberpunk-like gems that deserve mention
E.Y.E Divine Cybermancy
I'd even throw in the original Bioshock, it's steampunk, but has a very dark atmosphere.