I haven't seen nearly as many movies as some of you, so I created my own restrictions - I had to have seen at least 3 films from the director, and at least one had to be in my Top 100. This eliminated a lot of people I'd otherwise have very high, like Welles, Varda, Woody Allen, Antonioni, John Ford, and Kobayashi. There were a few eligible directors I left off because I'm not yet convinced they're great directors, from what I've seen.
#1 Akira Kurosawa Seven Samurai, Ran, High and Low, Yojimbo, Throne of Blood
#2 Federico Fellini 8 ½, La Dolce Vita, Nights of Cabiria
#3 Werner Herzog Grizzly Man, Fitzcarraldo, Aguirre, the Wrath of God, Little Dieter Needs to Fly
#4 Sergio Leone Once Upon a Time in the West, The Good, The Bad, and The Ugly, For a Few Dollars More
#5 Joel & Ethan Coen The Big Lebowski, Fargo, Raising Arizona, No Country for Old Men, Miller's Crossing
#6 Quentin Tarantino Pulp Fiction, Kill Bill, Reservoir Dogs, Jackie Brown
#7 Martin Scorsese Goodfellas, Taxi Driver, The Departed
#8 Billy Wilder Sunset Blvd., Double Indemnity, The Apartment
#9 Krystof Kieslowski The Three Colors trilogy, The Double Life of Veronique
#10 Francis Ford Coppola The Godfather, The Godfather, pt. II, Apocalypse Now
#11 Wong Kar-wai 2046, Chungking Express, In the Mood for Love
#12 Christopher Nolan Memento, The Prestige, Inception, Batman Begins
#13 Alfred Hitchcock Rear Window, North By Northwest, Psycho, Vertigo
#14 Howard Hawks Only Angels Have Wings, Rio Bravo, The Big Sleep, Gentlemen Prefer Blondes
#15 Peter Jackson The Lord of the Rings trilogy
#16 Michael Mann Heat, Miami Vice
#17 Terrence Malick Days of Heaven, Thin Red Line, The New World