NGE - with the last movie, some questions have been clarified and my theory confirmed, but I still did not understand many details. Also not after an extensive NGE-Wiki excursion.
Otherwise Ghost in The Shell.
Death Note. Did not look so many ... but may also be that I'm simply stupidly stupid xd
was quite difficult to understand relationships because I always looked like a two episodes and then felt no week Had ...
Classroom of the Elite The Anime was quite complex (but no comparison to the Light Novel there is nothing more)
and elves Song
At neon Genesis Evangelion I was totally confused, especially in the end. Similar to Hyouka and Eased or as at all time travel anime (s).
Serial Experiments Lain
The Perfect Insider