Well, for dark games the horror genre is your best bet.
1. I agree with Oblivion and add Morrowind. Morrowind is actually scarier and darker than Oblivion but Oblivion has more gore/ violence.
2. Silent Hill series. Any one of them is, literally, very dark.
3. Older Resident Evil games: the whole thing usually happens at night with a lot of scary stuff.
4. Manhunt. I know a lot of people think it to be nothing more but a violent punching bag to release your frustrations, but I found it to be very artistic in a dark way.
5. Mortal Combat series
6. Clock Tower series (horror game)
7. Nightmare Creatures. I played that long time ago on PS, but it stuck in my memory. The graphics would be really bad by today's standards though.
8. X3 is a pretty dark game (the space sim) because of the whole lonely space setting. It's got a high learning curve and I didn't like it all that much, but it did have a nice mood.
9. Aliens VS Predator 2: HIGHLY recommended! The graphics are old by now but still not too bad. Very dark and fun to play as predator.
10 Aliens Trilogy. I liked it as a kid. Others here don't think much of it. It is pretty dark though.
11. Hitman. Not scary or anything, but the storyline and the setting is always dark. What would do you expect from a game called Hitman.
12. Indigo Prophecy. It's not really dark, but more...heavy. I don'know if those two can be seen as the same.
13. Max Payne series. Very dark action. I got freaked out when in the first game he had to follow a line of blood while hearing his little dead daughter cry, or something along those lines. I would even call it horror.
14. Neverwinter Nights - Hordes of the Underdark expansion
15. S.T.A.L.K.E.R.
16. Twisted Metal series
17. That weird figting game where you used extremely gory ways to kill you really weird psychotic opponents in some mental institution. I forgot the name - it's an old game.
18. Prince of Persia Warrior Within.
19. Spawn series
Any game with an anti-hero promises to be pretty dark.
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