Hmm...I've found, mostly through experience rather than any preference per se, that I'm a DC kind of guy, or to be more precise, a Vertigo kind of guy. I used to think I preferred Marvel over DC. I also enjoy a lot of manga.
Let's see. Graphic novels I have enjoyed...
*V for Vendetta
*Batman (particularly The Killing Joke and Year One)
*The League of Extraordinary Gentlemen
I also have some Terry Pratchett graphic novel adaptations, as well as the Doctor Who comic compilations The Mark of Mandragora, and Oblivion.
As far as manga are concerned, my favourites are:
*Neon Genesis Evangelion (better than the anime series, IMO)
One of my most prized possessions is a copy of Watchmen, which I recently got signed by Dave Gibbons.
"What have you been doing since you stole that antique TARDIS of yours, since you first landed on Skaro? Shouting 'Look at me!!! I'm not fighting a war!', while you battle the Daleks all the way through space and time."