I haven't watched anime in a long time, mainly I can't find one that operates on a intellectual level.
The one that I have loved have been Ghost in the Shell (mainly for it's references to J.D. Salinger).
If anyone has any suggestions on incredible and intelligent animes, I am all ears.
Most of my favorite movies include Memento, Children of Men, Wristcutters, The Fountain, and basically any of Wes Anderson's films. Just to give you an idea of what I look for in media.