I have quite a few favorite ones.
"Who Took the Super out of Superman", Superman 149 (the original and best Death of Superman story), "War World" (DC Comics Presents 27-29), Alan Moore's Superman stories, All-Star Superman, Geoff Johns' Superman run, "The Unknown Supergirl", Supergirl's Sterling Gates' run, "Red Daughter of Krypton", "Supergirl: Being Super" and "Legion of Super-Heroes: The Great Darkness Saga" are some of my favorite stories starring Superman and his extended family.
"Batman: Year One" is my favorite Batman story, albeit I admit I haven't read a lot of them.
"Batgirl: Year One" and Batgirl 's Gail Simone run were quite good.
"Green Lantern: Rebirth was what introduced me to the Green Lantern mythos and made me a Hal Jordan fan.
Geoff Johns' Aquaman' run needs more love.