Here are some of my favorite stories and graphic novels. I'm more of a DC guy, so I'll let someone who's bigger on Marvel recommend the best Marvel stories.
Superman:
All-Star Superman
Kingdom Come
Birthright
Red Son
For The Man Who Has Everything
Whatever Happened to the Man of Tomorrow?
Godfall
Secret Identity
Why Must There Be A Superman?
For Tomorrow
The Jungle Line
The Last Son of Krypton
Superman and the Legion of Super-Heroes
Brainiac
Batman:
Batman: Year One
The Long Halloween
Dark Victory
The Killing Joke
Son of the Demon
Hush
Arkham Asylum: A Serious House on Serious Earth
The Man Who Laughs
A Lonely Place of Dying
Batman RIP
The Black Mirror
The Court of Owls
Gotham By Gaslight
Batman: Earth One
Wonder Woman:
Challenge of the Gods
A League of One
The Hiketeia
The Circle
The Flash:
Born to Run
Terminal Velocity
Blood Will Run
Green Lantern:
Green Lantern/Green Arrow Collection
Emerald Dawn 1 & 2
Emerald Twilight
Rebirth
Sinestro Corps
Mosaic
Willworld
Justice League:
DC: The New Frontier
JLA: Year One
Rock of Ages
Tower of Babel
Identity Crisis
I Can't Believe it's Not the Justice League
JLA/Avengers
Other DC Titles:
Sandman
52
Teen Titans: The Judas Contract
Titans, Young Justice: Graduation Day
The Legend of Aquaman
Animal Man (the current ongoing series)
Swamp Thing (ongoing)
Captain Atom (ongoing)
All-Star Western (ongoing)
I, Vampire
Saga of the Swamp Thing
Suicide Squad: Raise the Flag
Non-DC Titles:
Watchmen (okay, yes, it's published by DC, but not in the same universe)
Fables
Saga (ongoing)
Y: The Last Man
Invincible (ongoing)
100 Bullets
Hellboy volumes 1-5
Concrete
Irredeemable (ongoing)
The Walking Dead (ongoing)
Astro City volumes 1-5
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