Naruto is really the only Manga I read regularly anymore... because it is the only ongoing plot line that makes any coherent sense... and it appropriately masculine for my tastes. In the past I have enjoyed reading Death Note, and a countless others... but over all... a lot of Manga actually disappoint me in comparison to the anime counterparts. You might just call this a "lazy" complex... though rest assured I have read a fare share of good manga in my time.
One of the most disturbing I ever read was Barefoot Gen... an autobiographical manga written about the bombing of Hiroshima. It is very disturbing because all of it happened to directly, or to someone the author knew. I think that all politicians and nuclear weaponry advocates should read this manga. It certainly shifted even my already generally pacifistic views, and I think it is a very important part of world history for everyone to know. But again, I must emphasize that it is extremely disturbing! If you are not at least high school age, I would not recommend looking into it just yet!