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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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.
If you liked
Rurouni Kenshin: Meiji Kenkaku Romantan - Tsuioku-hen
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...then you might like
Shigurui
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Both anime are both samurai action films with fairly dark undertones at a slow pace. While Kenshin tends to lean toward more of a romantic drama, Shigurui has quite a bit more action and gore.
If you liked
Juubee Ninpuuchou
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...then you might like
Shigurui
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It took me a while to make the connection because I watched these two animes roughly 10 years apart from each other, but on second thought the only difference between the two is Shigurui is more drawn out (being a TV series) than Ninja Scroll, and it's samurai based action vs. ninjas. Both animes feature plenty of action, political background development, dark tones, gruesome deaths, and gratuitous sex scenes sprinkled throughout.