I'll hit some that others haven't yet instead of just going with the old Standbys
Top Ten: Alan Moore presents a Super Hero Cop Show in comic book form, it's about the sparkling city of Neopolis where all the "science heroes" in the world live out lives as ordinary as they can given the intense strangeness of it all. The officers of Top Ten (the tenth precinct in an Interdimensional Police Organization) are charged with keeping the peace. I'd go with the two main volumes and The 49ers, Smax the Barbarian is super strange and the rest wasn't written by Alan Moore. This is a favorite among people who do and do not love super hero stories, it's got amazing art, a good story and great characters.
Atomic Robo: Proof Positive how brilliant All Ages Comics can be... Atomic Robo is written by Brian Clevenger (of 8-bit Theater fame) and drawn by Scott Wegener. It's about Robo, a Robot invented by Nikola Tesla in 1923 and his adventures across the 20th Century and beyond. It's old-school Doc Savage-esque Pulp Adventure with a great sense of humour and adventure. All of the books tell individual stories that conclude at the end of the trades but there is an ongoing continuity. There are 7 Volumes so far with the 8th coming out soon. It's hard to recommend them individually because dayum... they are all super good.
All Star Superman: Grant Morrison and Frank Quitely present the BEST Superman story ever, it's essentially a 12 Issue/2 Volume limited series about the death of Superman and a general love letter to the best of Superman. The story is that Lex Luthor has succeeded in "killing" Superman by over exposing him to the suns radiation that gives him his power in the first place, thus The Man of Steel is slowly dying but growing smarter and stronger as he does. This is packed to the gills with action, fun and intense humanism.
Mouseguard: Written and Drawn by David Petersen, Mouseguard tells the story of The Mouse Territories and their intrepid protectors, The Mouseguard. The art is gorgeous, the fantasy world of the Mouse Territories is stunning and the sheer DRAMA is pretty damn powerful... think The Secret of Nymh meets Redwall (except the Mice are actually Mouse Sized).
Bone: Written and Drawn by Jeff Smith, Bone is the bizarre combination of the old fashioned cartoons of Walt Kelly and Lord of the Rings and it regularly swings from Goofy Comedy to Dark Epic Fantasy. I would recommend the color version over the black and white, despite Smith's mastery of Black and White, because in color it looks like the most amazing animated film that... isn't actually an animated film.
Shazam versus The Monster Society of Evil: Jeff Smith draws and writes DC Comics' Shazam/Captain Marvel character, its gorgeous, funny, amazing and self contained. Seriously, read this damn book... it's so good and so funny.
Batman: The Long Halloween: My favorite Batman Story, details a year long mystery and goes over the origin of Two Face in exciting new detail. A great examination of Batman as a detective and a key inspiration for The Dark Knight with its depiction of the new Supervillains of Gotham clashing with the old Mafia.