Brian K. Vaughn's Pride of Baghdad is among the most amazing graphic novels to come out recently. Its a haunting anthropomorphic tale of a group of lions the escaped the Baghdad zoo in the wake of the US invasion, it really will stick with you.
If you haven't already checked it out, Alan Moore's The Watchmen is one of the most important books in coomic history for its rich story telling, realistic characters, and mature themes. Its a superhero book, but it really deconstructs the whole "What is a Superhero?" question.
Lucifer, a Sandman spin off which recently ended, was great, in my opinion. Written by Mike Carey, it was interesting and was done in a way that would have humbled Milton as far as what kind of a character Lucifer was.
Deadman, which was recently launched in Vertigo with Bruce Jones helming it has been interesting. Its only got two issues out, but so far its been bloody brilliant. It plays with Super String Theory and death through out reality. Still, only two issues are out so far, so its hard to get a read on it.
Testament, by Douglas Ruckshoff is a brilliant biblical-ish story. It takes the Hebrew Scriptures and applies them to a post-modern story. It shows how parrells can be drawn between the two. Its coming up on Issue 11, and the first trade was recently released.
These aren't necesarily all cyber punk or Apocalyptic, but they're all amazing reads. I'd really just suggest checking out Vertigo in general, its got some of the most intelligent and intriguing stories in comics.
If you really want to diversify, though, in DC proper (Vertigo's an imprint of DC), I'd check out Identity Crisis. Its certainly a smart book, written by New York Times best selling author Brad Meltzer. It involves Superman, Batman and all of them, but it has them dealing with the death of Elongated Man's wife (Elongated Man being a Justice Leaguer who left and was married for a very long time), and things internalized in the Leage of their past indiscretions and secrets that rupture the League at its core.