Batman: Year One, The Long Halloween, Dark Victory, Death in the Family, Hush, R.I.P

Superman: Man of Steel (1986), Panic in the Sky, Death of Superman, Reign of the Supermen, Birthright, All-Star Superman, For the Man who has Everything, New Krypton, War of the Supermen, Brainiac

The Flash: Waid and Johns’ run on Wally West has most, if not all the best Flash stories to date (Rogue War, arc with Zoom, etc.), for Barry, anything post-Flash: Rebirth, Flashpoint, some of the New 52 run

Green Lantern: GL: Rebirth (pre-flashpoint), Johns’ run, Sinestro Corps War, Blackest Night, War of the Green Lanterns, Rise of the Third Army, etc

Aquaman: The entire New 52 and Rebirth runs will cover that.

Wonder Woman: The Post-Crisis run has some of the best storylines i.e. The Hiketeia, post-IC will have a few good ones too.

Justice League: Waid and Morrison in the 90s has the best storylines for the JLA, including Rock of Ages, Tower of Babel and the Obsidian Age

Green Arrow: The Longbow Hunters, the post-Zero Hour run, Rebirth run

DC as a whole: COIE, Infinite Crisis, Final Crisis, Blackest Night, Forever Evil, Metal, Our Worlds at War, 52,