 If you liked
Speed Grapher
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 ...then you might like
Darker than Black: Kuro no Keiyakusha
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Both shows contain a somewhat "dark" atmosphere with a lighter tone appearing now and then. Each has a "secret" organization that rules the city. Each also has a sort of "special power gene" that only certain humans can obtain. This gives the characters in both series new skills and abilities. With interesting plot lines, both of these will keep you glued to your chair.
In both shows, certain individuals have unique super-powers thanks to a recent phenomenon. In Darker than Black, you have factions of these people up against one another. In Speed Grapher, it's one man against everyone else, a more exciting setup IMO. Also, the characters in Speed Grapher are less opaque than those in Darker than Black where the mystery usually takes precedence over the story, leaving so much unexplained that the show gets tedious.
Similar theme, atmosphere, metaphysics governing supernatural powers, story progression and pacing. Both shows take place primarily in a "dark" city controlled by the underground where the main character fights against an omnipresent shadow-organization, filled with various goons who've derived powers based on their character flaws, in order to protect the freedom of a sheltered girl. The theme of science causing god complex is central to either story. The music used in both also strikes me as similar in style, composition and atmospheric use within the anime.
Both series have a similar feeling as they have rather dark atmospheres, characters with special powers, and a loli sidekick (who is someone that the MCs need to protect). There are some other various similarities that both series have which really make one anime feel like the other.
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Recommended by RafaelDeJongh
Both anime contain a dark atmosphere and have a secret organization to unmask. A few people have a "strange virus" that can be activated and can give to them strange powers. Both do no have a foregone conclusion.
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Recommended by revengerofdeath