Dark and intelligent Sci-fi anime are by far my favourite anime, or really any show at all, live action or not.
Im trying to put a list together of "all" of them so I can know which I havent seen and check them out.
I'll Kick off the list, but hopefully you gall can fill in the gaps:
Akira
Cowboy Bebop
Serial Experiments Lain
Evangelion
Psycho Pass
Steins; Gate
Ergo Proxy
Darker than Black
Tokyo Ghoul
Deadman Wonderland
Elfen Lied
Ghost in the Shell (original Movie... I havent seen any others)
Full Metal Alchemist (sort of the PG version of Dark but still...)
Black Bullet
EDIT 1:
[quote]
Parasyte
Death Note
Attack on Titan
Dollhouse (live action)
Neon Genesis Evangelion
Texhnolyze
Mobile Suit Zeta Gundam
Bokurano
Blue Gender
.hack//Sign
RahXephon
Guyver: The Bioboosted Armor
[/quote]
EDIT 2: [quote]
Madoka Magica
Haibane Renmei (starts off pretty happy, but its totally different by the end)
Another
Higurashi
Future Diary/Mirai Nikki
Monster
[/quote]
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Hellsing ultimate is pretty dark