I'll give this a shot.
Superhero comic:
Astro City :: I'd say Life in the Big City as it's the first but really all of them. I especially like The Tarnished Angel. More than any other comic I think it brings Superheroes to life. There are so many stories that deconstruct the Superhero. I think Astro City is the superhero stories that rebuild them.
Non-Fiction:
Maus :: Obvious choice. It's a stunning comic that really shows what can be done outside the normal genre of comicbook fiction writing.
Mature Readers:
Animal Man :: When I first read the three volumes I was completely blown away. It is smart, horrific, challenging, funny and loveable. Even caused me to think about Animal Rights in ways I hadn't before. It works on so many levels and I can always go back and re-read it.
Other? (Since I don't read Manga I can't comment and going by Elijya's categories I couldn't see a place where this fits.)
Bone :: With the one volume edition there is no reason people shouldn't read this. It's seminal; a dark, humourous, touching, sprawling epic tale. Which really lives up to every bit of hype it gets. It's simply stunning.
Retro:
Dennis O'Niel/Neal Adams' Green Lantern/Green Arrow :: I'm not sure I can say anything that hasn't been said before about this. It was one of the first steps to how comics are today.