This is the fun part. In order to simplify things a bit, continuity has been broken into chunks. This isn't perfect, as continuity is in the eye of the beholder. I do not try to discredit any story, as most everything is "in continiuity" at some point or another. I have done my best to reconcile any problems / contradictions by placing everything I can.

"The original Crisis took all the remaining Earths and merged them together again. But there were glitches... paradoxes... and the universe demanded that it's flaws be fixed. With each strike he's (Superboy Prime) sorting his way through the conflicting permutations... resolving all the possible realities. This is... miraculous. I don't know how, but he's altering reality out there (on Earth). Creating conflicting truths. People are changing without explanation. New events are superseding what had always been. Each strike he takes is rupturing the continuity of life without reason or purpose. In this place we can alter our own reality, but now we're changing theirs, too."
-Alexander Luthor, Infinite Crisis Secret Files & Origins

For a current Hyper-Timeline and Infinite Continuity pdf, click here. Updated December 2008.

Section 1: Beginnings
Superheroes begin to appear across the globe. Years after the Justice Society of America disbands, Superman debuts in Metropolis. Batman begins his crime-fighting career in the shadows of Gotham City. Dick Grayson emerges as Batman's first partner, Robin.
Section 2: Partners
The Justice League and Teen Titans form. Robin becomes Nightwing; Jason Todd becomes the second Robin.
Section 3: Tragedies
The multiverse is destroyed and Barry Allen (the Flash) is killed. Jason Todd dies at the hands of the Joker while searching for his mother. Wonder Woman is reborn. Billy Batson receives the powers of Shazam. Wally West, formlerly Kid Flash, takes over as the Flash. Talia al Ghul claims to miscarry Batman's child. Tim Drake becomes the third Robin.
Section 4: Other Batmen
Superman is killed by Doomsday. Azrael and Nightwing fill in as Batman after Bruce Wayne's back is broken by Bane. Kyle Rayner becomes the Green Lantern of Earth. The Crisis in Time (Zero Hour) occurs.
Section 5: New Purpose
Bruce Wayne returns as Batman. The demon Neron attacks Earth. A wave of plagues, set in motion by Ra's al Ghul, strikes Gotham City. Hal Jordan sacrifices himself in order to save the Earth. Clark Kent marries Lois Lane.
Section 6: Gotham Destroyed
The Justice League of America reforms. Superman's powers change splitting him into two energy beings. Gotham City becomes a No Man's Land after a huge earthquake hits.
Section 7: Masterminds
Lex Luthor is elected President. Commissioner James Gordon, one of Batman's oldest allies, retires after being shot. Oliver Queen returns from the dead. Bruce Wayne is framed for the murder of his girlfriend. A new enemy attacks Batman, calling himself Hush.
Section 8: Infinite Crisis
Superman's cousin is discovered on Earth. The JLA's "mindwiping" incident is uncovered. Hal Jordan returns as Green Lantern. Jason Todd, the formerly dead second Robin, returns as the murderous Red Hood. Stephanie Brown becomes Robin after Tim Drake gives up his costume, only to be killed by Black Mask; Tim reclaims his secret identity. Survivors of the original Crisis return hoping to recreate the perfect Earth.
Section 9: New Earth
A year passes without Superman, Batman, or Wonder Woman. Oliver Queen is elected mayor of Star City. Superman's powers return, as do Batman, Robin, and Nightwing. Bart Allen becomes the Flash and is later killed. Wally West returns from the Speed Force. Selina Kyle, Catwoman, gives birth. It is revealed that Batman has a son from a short-lived marriage to Talia al Ghul.