If no-one else has said at least one of these yet, my work is done
Obvious:
Kick Ass (yes there is a sequel, currently serialised in CLiNT magazine)
Batman - Dark Knight etc
Transmet
Akira (this'll take you a while) << for the record, the movie cuts off somewhere in the middle of book 3 of... 6? 7? in the master collection, and mashes SO much of the fine detail together.
Sandman
Watchmen / V for Vendetta / moore-stuff in general
Hell, I've only read maybe half of those, but I've seen bits and bobs of the others and wished that I'd had the time to plough through whilst they were close at hand.
Less obvious but probably already mentioned:
Maus should be required reading on the school curriculum
Persepolis is along similar lines but not quite as grim.
Bone... if you have the patience.
Ghost in the Shell ... it was a good anime, but an AWESOME manga (the same effect as Akira but on a smaller scale - lots of stuff went missing), and the paper version has dated far better than the movie.
Various other Shirows (author of GitS) - they can be hit and miss, so if you don't like one, ditch it and sample another.
Tank Police, Black Magic, Appleseed, all pretty cool. Strangely the "side story" volumes are at least as good if not FAR better
Probably not mentioned? (more detail with these)
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The Adam Warren version of The Dirty Pair. It's trashy and just one massive excuse for him to draw cheesecake, but by heck is it enjoyable. A fair bit of proper hard-science fiction in there too, bubbling away under the surface but - much like Cowboy Bebop after it - never becoming the main focus or overtaking the dramedy that is the thing's driving force.
(Also his more original
"Empowered" is pretty good)
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Paradigm Shift - an american drawn manga that started life on the web ... no, don't run off! It's goddamn brilliant, and the print copies are cheap (alternatively: badger your local library to get it in and spread the love). It is released on a terribly slow schedule though, much like Akira was (and NotVoW - see later). There's not a great deal I can say about it that doesn't ruin the plot twists, so just consider what would happen if the X-Files, CSI and Law & Order crashed together at an intersection in downtown Chicago.
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Girl Genius has a more traditionally comicky (but watercoloured!) style and went through a bit of a fanzine - webcomic - mixed media evolution, but is good. Think: voluptuous steampunk dramedy epic.
*
Nausicaä of the Valley of the Wind is something to move onto after you've built your staying power with Akira and a taste for manga and far-flung settings with some of the others. Think: Hayao Miyazaki hand draws several thousand pages of his own epic manga. Think: world suffering from catastrophic, global, manmade ecological collapse and all the conflict that comes with. Think: jet scooters. Think: Scrappunk. Fox-squirrels. Bearded swordmasters. Teenage girl with unfeasibly large bosom (always dressed in winter clothes, though) attempting to save the world FROM ITSELF.
It's complicated. It's in 4 volumes. You'll have to re-read it a couple times, particularly if you want to properly soak up all the detail in the artwork after getting the gist of the story. You may have to mentally grapple with Nausi herself being an obvious, Tumnus-grade Christ analogue. It's worth it.
* Oh, and so many various damn good web comics have had print runs, but whilst they're available free online you may as well explore for yourself... For something different and as an example plucked entirely at random, try
"Lackadaisy". 1920s gangster... cats. With gorgeous sepia-toned art. It's quite lightweight, and for now, fairly short in terms of amount published, so could be a coffee-table book.
Edit: Oh god, is there NOTHING here that no-one else has said about?

Consider it all VOTES for them, then.
Also go just browse the library graphic novel section and flick through a few, see if anything catches your eye.
For extra trashy, eye rending colour, pulp sci fi awesomeness, see if they have any compilations of the old "Amazing Science Fiction" comics and similar. My dad used to read those, I looked through them when he was done, they're ... mad. Mad, bad, and UTTERLY BRILLIANT.