Hurm. Well, Wolf's Rain is certainly apocalyptic, but not really 'creepy'... Not the sort of headfuck, say, Serial Experiments Lain is designed to deliver. But yeah.
Thinking about it now that I've just recently started watching it again, Ergo Proxy might actually be a pretty good fit. It's a cyberpunky detectivey slow burner that is a bit hard to reccomend to most, but I think it has the right kind of mystery plot to fit in with what you mentioned before.