If you liked
Koukaku Kidoutai: Stand Alone Complex
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...then you might like
Darker than Black: Kuro no Keiyakusha
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Both share a similar style where a greater storyline is carried on by seemingly unrelated episodes (or episode pairs in the case of Darker than Black).
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Recommended by luinthoron
Show is episodic in nature for the most part and is a crime/drama as well.
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Recommended by ElectricSlime
They both have an episodic "crime of the week" format combined with a long-term story arc. There are sometimes similar plots, and both explore the idea of people who are somehow different from ordinary humans (cyborgs in GITS, people with superpowers in DTB). Both are intelligent (moreso GITS), dark (moreso DTB), and mature and have kickass soundtracks by Yoko Kanno.
Both, Darker than BLACK and GiTS: Stand Alone Complex have similar plot build ups. While each episode seems mostly independent of the other on a deeper almost all episodes are related in some way. Also both revolve around a team protagonists (although admittedly both teams has its own protagonist)
These two animes revolve a protagonist with a strong support team in a political and action thriller featuring unique powers (although that's a given in most animes).
While Ghost in the Shell series revolves more around a central political plot, Darker than BLACK asks similar metaphysical questions underlying Ghost in the Shell.
Both are based around teams in secret organisations investigating and participating in missions.
Similar style of case by case operations, with undertones of something more serious going on.
Both groups have specialists in their teams based on resources and abilities that aren't available to general public, some of which must be kept secret.
International governments/organisations trying to manipulate and control information and access to resources.
Both series look over the implications on society after drastic changes to what being human means.
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Recommended by BlackVirtue