 If you liked
Nijigahara Holograph
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 ...then you might like
Serial Experiments Lain: The Nightmare of Fabrication
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Both have a very dark and intricate plot. They mess with your mind and offer many interesting ideas. They delve into psychological and philosophical aspects. The plots have multiple interpretations and may take a while to fully understand. The style is extremely surreal, abstract and completely different from anything else.
Since you can't recommend an anime for a manga this Lain oneshot is the closest thing to the Lain anime so if you liked the Serial Experiments Lain [i]anime[/i] you'll prolly enjoy Njigahara Holograph.