I haven't read too many manga, but I'll throw out a few suggestions.
I really enjoyed Akira, especially because I don't get the hype over the film. The manga version is about 6 decent sized books long and because of the increased detail and time available to tell the story it makes it much more satisfying. It's a much more epic story in the manga version too.
In some ways, I've liked the Neon Genesis Evangelion manga more than the series, it's a lot more focused and cuts out most of the sillier humor from the anime. It's also fairly different in many ways right from the start, though in keeping with the same ideas of the anime. It's still not done yet, after about 14 years... There is something like 11 volumes out now, regular size, the author is just very, very slow. I'm curious to see how he ends it and how much it'll be like either the series or movie. Or perhaps something new.
The Scott Pilgrim series. Not a manga, but a Canadian comic done in manga-style. I was recently introduced to this series and it's so much fun. If you have any knowledge of video games, anime, and/or geek culture you should try it out. It's about Scott Pilgrim, a relatively regular 23 year old slacker, who is in a band and gets a mysterious girlfriend, but to keep the girlfriend he has to defeat her evil exes in battle. As ridiculous as it sounds, it's really great. There are 5 volumes out now of a planned 6. I've read up until 4, just recently got 5, and I'm in love with the series.
That's what I got for you now, maybe I'll remember some others later.