If you liked
Appleseed (Movie)
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...then you might like
Vexille: 2077 Nihon Sakoku
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Both by the same producer and explores the notion of bio engineered humans and other such possibilities. Although, Vexille is slightly more about the ethics of such research and experimentation. But both are equally good movies.
If you liked
D.Gray-man
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...then you might like
Fullmetal Alchemist
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Despite having very different goals, both manga have some similarities. Such as the physical similarities between Ed and Allen as well as the running theme of Good vs Evil. However, D.Gray-man has a "religious" aspect in the manga, while FMA was based upon science and alchemy.
If you liked
Witch Hunter Robin
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...then you might like
Ergo Proxy
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Both have similar dark tones in their story lines, as well as a very deep psychological aspect. As well as a similar style in art and experiences with the "supernatural". It also helps that both anime have the same director ;)
If you liked
Zettai Kareshi.
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...then you might like
Imadoki!
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Both have similar romantic plot lines - but with a hint of underlying comedy. A must read if you like Watase-sensei's work.
If you liked
Imadoki!
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...then you might like
Fushigi Yuugi: Genbu Kaiden
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Both are by the same author, but with dramatically different plot lines. Despite this, there is a similar feel to both manga. A must read if you like Watase-sensei's work.
If you liked
Giniro no Kami no Agito
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...then you might like
Toki wo Kakeru Shoujo
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Similar elements concerning time travel (of a sort) and the differences between the past and the present.
If you liked
Kimi ga Nozomu Eien
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...then you might like
Saishuu Heiki Kanojo
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Both were initially set as a high school drama. Both have interesting love triangles (although Kimi ga Nozomu Eien doesn't have that whole end of the world thing). Striking similarities between the two, both are excellent dramas and both are well worth watching!
If you liked
Samurai Deeper Kyou
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...then you might like
The Silvery Crow
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Both mangas are the work of Akimine Kamijyo. This being the successor to the famous Samurai Deeper Kyo manga. Both feature the same fantastic art style and the comedy moments (although, silvery crow seems to have a lot of those at the moment) as well as some well developed characters.
If you liked
Bleach
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...then you might like
Zombie Powder.
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The most popular of Tite Kubo's two manga creations (Zombie Powder being the first) but in reading his previous manga, you can clearly see how he perfected his incredible art style, as well as awesome character design for Bleach. I actually started reading Bleach first and read ZP afterwards, and you can clearly see that there are similarities between the two manga, however, some might not be as apparent as others. Both mangas have amazingly detailed battle scenes, the super-cool characters (that are vital for a good manga) and the superb plot line that ties the whole thing together. First published in 2001 and still going strong - the length of this manga makes up for any disappointment at the abruptness of Zombie Powder's end.