General DC

- DC •
Batman/Superman/Wonder Woman: Trinity (Matt Wagner) First meeting and alliance between Wonder Woman, Batman, and Superman.
Blue Beetle v7 #1-current (Keith Giffen. John Rogers, Matt Sturges) - A teenager finds an alien scarab that gives him a super suit, which he uses to fight crime.  
Booster Gold v2 (Geoff Johns) - Booster Gold and the Blue Beetle team up. Awesome ensues.
Checkmate V2 #1.25 (Greg Rucka) - "Take a big chunk of The OMAC Project, take the concept of "Who Watches the Watchmen?" and throw in some James Bond and you've got Checkmate." (quote from Rucka himself)  
DC: 52 (Geoff Johns, Grant Morrison, Greg Rucka, and Mark Waid) - 52 issues, one per week for a year, describing what happened in the year following Infinite Crisis.
Doom Patrol v2 #19-63 (Grant Morrison) - Bizarre. Surreal. Kickass.
Elseworld's Finest (John Francis Moore) - Bruce Wayne was never Batman. Kal-El died before he could become Superman. Batgirl protects Gotham with an iron fist, and Supergirl teams up with the Justice Society... oh. and Lex Luthor.
Final Crisis: Rogues' Revenge (Geoff Johns) . The Rogues seek vengeance on Inertia after being used in the killing of Bart Allen.
Formerly Known as the Justice League (Keith Giffen and J.M. DeMatteis) A team of superheroes calling themselves the "Super Buddies" and trying to be more "accessible to the common man."
Giantkiller (Dan Brereton) • Genetically engineered supersoldier uses biotechnology and a katana to fight giants the entire military couldn't defeat.
Green Arrow: Quiver (Kevin Smith) • Oliver Queen gets brought back from the dead with only his memories prior to Longbow Hunters intact. He then tries to find his place in the world.
Green Arrow: Year One (Andy Diggle) Tells of the origins of the Green Arrow, and how Ollie Queen started to give a damn.
I Can't Believe It's Not The Justice League (Keith Giffen and J.M.Dematteis) - Sequel to "Formerly Known as the Justice League."
JLA #1-41 (Grant Morrison) - A team of superheroes forms, the primary members of which are Superman. Batman. Wonder Woman. Aquaman. the Flash, Green Lantern. and Martian Manhunter.  
JLA/Avengers #1-4 (Kurt Busiek) - JLA and Avengers are manipulated into fighting each other on a scavenger hunt of monumental proportions. This is much cooler than it sounds.
JLA: Age of Wonder (Adisakdi Tantimedh) - Superman lands in Kansas in the 1850s. Supes and Tesla work together. There's a Death Ray.  
JLA: Shogun of Steel (Ben Raab) JLA in feudal Japan. Hell yes.
JLA: The Greatest Stories Ever Told [collections] Self-explanatory. Collections of the best JLA stories.
Jonah Hex (Justin Gray and Jimmy Palmiotti) - Western about Jonah Hex, a bounty hunter, follows him through the American West. China and South America.  
JSA: The Golden Age (James Robinson) - Elseworlds depicting an alternate history for the Justice Society of America.
JSA Kingdom Come Special: Magog (Peter J. Tomasi) Backstory of Lance Corporal David Reid, who eventually became Magog.  
JSA Kingdom Come Special: Superman (Alex Ross) - Superman vs. Superman.
JSA Presents: Green Lantern (Steven T. Steagle) Collection of modern stories written about the original Green Lantern... Alan Scott.
Justice (Alex Ross) - JLA faces down the Legion of Doom. Every supervillain is motivated by the same dream of the planet's destruction and is trying to avoid it.  
Justice League: The New Frontier (Darwyn Cooke) - Animated movie about the Justice League. That's really all I can tell you without spoilers.
Justice League Elite (Joe Kelly) . A group called the Justice League Elite is formed to attempt black ops that the JLA can't be seen to be involved with. Members include Sister Superior, Coldcast, Menagerie II. Manitou Raven, Green Arrow. Flash (Wally West). Major Disaster. Katsumi (you'll see), and Naif al-Sheikh.  
Justice Society of America v2 #1.87 (James Robinson. David S. Goyer. Geoff Johns. Paul Levitz) . Second volume of JSA.  
Justice Society of America v3 #1-current (Geoff Johns) • Third volume of JSA.
Kingdom Come (Alex Ross) - "Traditional- superheroes vs. amoral vigilantes 20 years in the future. Batman and a team he assembles are trying to stop the conflict from escalating further. while still taking on Lex Luthor.
Manhunter (Marc Andreyko) - Kate Spencer, a prosecutor sick of superhuman villains getting away with things. constructs a supersuit and hunts them down.  
Ronin (Frank Miller) - Cyborg posessed by an ancient samurai hunts a demon that escaped from an enchanted sword.
Sandman Mystery Theatre (Matt Wagner and Steven T. Seagle) - A human vigilante called the Sandman fights crime with a gun that fires sleeping gas. Not to be confused with Neil Gaiman's Sandman.  
Seven Soldiers (Grant Morrison) - A new version of the Seven Soldiers of Victory fight to protect Earth from the Sheeda.
Shazam! - The Monster Society of Evil (Jeff Smith) Update of Captain Marvel's backstory.
Space Ghost (Joe Kelly) • Origin of Space Ghost. Has a few subtle (and not-so-subtle) nods to Space Ghost Coast to Coast.
Starman (James Robinson) - Jack Knight (the son of the original Starman. Ted Knight, and brother of David Knight), initially has disdain for superheroes. but after his brother is killed, he uses one of his father's old gravity rods to escape a similar fate. He then tracks down his brother's killer to protect his father.  
Swamp thing v2 #20-64 (Alan Moore) - Moore revamps Swamp Thing, taking it from mediocre to magnificent.
The Spirit #1.23 (Darwin Cooke) - A masked vigilante fights crime as The Spirit. The twists and turns and genre-hopping is what makes this brilliant.  
The Spirit Magazine (Will Eisner) - More stories about The Spirit.
The Spirit Special #1 (Darwyn Cooke) - More stories about The Spirit.
The War that Time Forgot (Bruce Jones) American soldiers are stranded on an island inhabited by Dinosaurs.  
Trinity (Kurt Busiek) . Weekly comic series starring Batman, Superman. and Wonder Woman.
Watchmen (Alan Moore) • Amazing deconstruction of the superhero genre with memorable characters and complex, human problems. Brilliant.
- BATMAN
Batman #667.669 (Grant Morrison) • The fates of non-powered superheroes from the past around the globe are revealed.
Batman & Superman: World's Finest (Dave Gibbons) - Batman and Superman team up.
Batman: Arkham Asylum: A Serious House on Serious Earth (Grant Morrison) - The patients take over Arkham Asylum and are going to murder the staff unless Batman meets with them.  
Batman: Arkham Asylum: Living Hell (Dan Slott) - Provides a detailed look at Arkham Asylum from several points of view.
Batman: Black & White [collections] - Numerous short but awesome stories of Batman told in (you guessed it!) black and white.
Batman: Dark Victory (Jeph Loeb) Sequel to Batman: the Long Halloween. described later in this list.
Batman: No Man's Land (various) A major earthquake hits Gotham City, and the U.S. government evacuates the city and abandons those who choose to stay. No Man's Land covers the story of the residents in isolation until the city is re-opened and rebuilt.  
Batman: The Ring, The Arrow, and The Bat [collections] - Green Arrow gets involved in a civil war in the Far East. He and Green Lantern help the rebels. Years later, the general they defeated has regained  
control of the country and captures 011ie. planning to execute him. Batman infiltrates the general's base to save the Green Arrow. This includes the first meeting of the Green Arrow and Batman.
Batman: The Doom That Came to Gotham (Mike Mignola) - Batman + the Cthulhu mythos. Good stuff.
Batman: The Greatest Stories Ever Told Vol. 1 & 2 [collections] - Collections of the best Batman stories.
Batman: The Killing Joke (Alan Moore) - Probably the most influential comic about the Joker. The Joker's latest crime (his most vicious yet) is told interspersed with flashbacks of what may have been his life before he became the Joker.  
Batman: The Long Halloween (Jeph Loeb) Early in Batman's career as a crimefighter, he races against the clock to capture a criminal who kills one victim a month, on a holiday each time.  
Batman: The Man Who Laughs (Ed Brubaker) Batman's first post-Crisis meeting with the Joker. Joker Venom is introduced.
Batman: War on Crime (Paul Dini and Alex Ross) - Introspective look at Batman as he catches a robber, but is unable to save a husband and wife who run a grocery, leaving behind an orphan. The situation is somewhat similar to the one that caused Bruce Wayne to become the obsessed crimefighter he is.  
Batman: Year One (Frank Miller) [Batman #404-407] - Retelling of Batman's origins.
Gotham Central #1-40 (Ed Brubaker and Greg Rucka) • A series focusing on the police in Gotham City.
Realworlds: Batman (Tom Sniegoski and Christopher Golden) • Moving story of Charlie, a mentally handicapped 27 year-old who loves the camp 1960's Batman, and how he reacts to a girl he was friends with as a child. It's about his coming to realize that things aren't always the way they seem in his old Adam West TV series. The Batman movie conies out and Charlie realizes sometimes you have to do things you don't always want to. to get the job done.  
GREEN LANTERN
To get caught up (Much of this is too interwoven to be able to write clear descriptions for each part without spoiling the story.):
Green Lantern: Rebirth (Geoff Johns) - Not considered among the best of Johns' work, or the best of Green Lantern stories, it is nonetheless relevant to his backstory.
Green Lantern Corps: Recharge (Geoff Johns and Dave Gibbons) - Lots of new recruits, and the Green Lanterns fear they may become involved in a war.
Ion: Guardians of the Universe  
Green Lantern #1.20
Green Lantern Corps #1-13  
Sinestro Corps War:
Sinestro Corps Special #1
Green lantern #21.
Green Lantern Corps #14  
Green Lantern #22
tales of the Sinestro Corps: Parallax #1
Green Lantern Corps #15  
Green Lantern #23
Green Lantern Corps #16
Tales of the Sinestro Corps: Cyborg-Superman
Green Lantern #24
Green Lantern Corps #17
Tales of the Sinestro Corps: Superman-Prime #1
Green Lantern Corps #18
Green lantern #25 Sinestro Corps finale
Tales of the sinestro Corps: Ion #1
Green Lantern #26-35
Green Lantern Corps #19031
Final Crisis: Rage of the Red Lanterns
Green Lantern #36-ongoing  
Green Lantern Corps #31-ongoing
Other good Green Lantern stuff:
Green Lantern/Green Arrow (Dennis O'Neil) - Green Arrow and Green Lantern face off.
Green Lantern: Emerald Dawn (Keith Giffen and Gerard Jones) - Hal Jordan's origin story.
Green Lantern: Emerald Dawn II (Keith Giffen and Gerard Jones) - Sequel to (you guessed it!) Emerald Dawn. following Jordan's 90-day jail sentence.  
Green Lantern: Fear Itself (Ron Marz) - Alan Scott, Hal Jordan, and Kyle Rayner each face the same monster, which shows them their deepest fears.
Green Lantern: Legacy - The Last Will & Testament of Hal Jordan (Joe Kelly) - Story reflecting upon the life of Hal Jordan.
Green Lantern: Willworld (J.M. DeMatteis) - Story of how Hal Jordan mastered his power ring, taking place on a world formed entirely from the creations of other Green Lanterns.  
Green Lantern V3 #46-50 (Gerard Jones and Ron Marz)
- SUPERMAN
Action Comics #837-current
All-Star Superman (Grant Morrison) - Superman reimagined in an alternate reality. Updated but still classic Superman.
Superman #650-current
Superman/Shazam First Thunder (Judd Winick) - The first meeting between Superman and Captain Marvel.
Superman: For the Man Who Has Everything (Alan Moore) [Superman Annual #11] - Superman and Batman are each shown their "hearts' desires" during which time they are helpless. Meanwhile, Mongul is attempting to conquer the universe.  
Superman: Infinite City (Mike Kennedy) - Kai-El wasn't originally going to be headed for Earth. Supes finds a pocket dimension based on Krypton.
Superman: Kal (Dave Gibbons) - Kal-EI lands in medievail England.
Superman: Last Son of Earth (Steve Gerber) - Clark Kent is launched to Krypton in a rocket from the doomed planet Earth. He finds a Green Lantern power ring.
Superman: Peace on Earth (Paul Dini and Alex Ross)
Superman tries to take on world hunger.
Superman: Red Son (Mark Millar) - What if Superman had been raised in the Soviet Union?
Superman: Secret Identity (Kurt Busiek) • Clark Kent's just this guy in the real world. Superheroes are fiction. Suddenly he gains Superman's powers.
Superman: The Greatest Stories Ever Told volumes 1 & 2 [collections] • A collection of the best Superman stories.
Superman: War of the Worlds (Michael Lark) - H.G. Wells'"The War of the Worlds..." with Superman!
Superman: Whatever Happened to the Man of Tomorrow? (Alan Moore) • Retiring of the original Superman prior to the John Byrne reboot.
Superman: What's So Funny About Truth, Justice and the American Way? (Joe Kelly) [Action Comics #775] - Superman takes on a group called The Elite. who are ultra-violent anti-heroes that viciously kill their foes.