Kurosawa, Tarantino, Ridley Scott, and Spielberg are just a few favorites already mentioned, so I'll pick a few left out.
Stanley Kubrick is my main man. His resume is a roster of some of the most famous and influential films ever made, and he made less than 15 of them in his life:
2001: A Space Odyssey
The Shining
Full Metal Jacket
A Clockwork Orange
Dr. Strangelove: or How I Learned to Stop Worrying and Love the Bomb
just to name a few
Sidney Lumet is a damn fine choice; the great chameleon made some dynamite work and he managed to do it with his own inimitable but ever-changing approach each time. In many ways he's the anti-auteur but becomes one in the process:
Network
The Verdict
12 Angry Men
Equus
The Pawnbroker
Andrei Tarkovsky. The Russian genius who can actually contend with Kubrick for breathtakingly unique and powerful images. I started on him with Stalker and I've never been the same since.
Stalker
Mirror
Nostalgia
The Sacrifice
Andrei Rublev
John Carpenter and John Landis were both two of the best genre filmmakers in the USA until the last decade or so when Carpenter went into filmmaking-as-a-hobby phase with his Showtime Masters of Horror movies and Landis toiling in relative obscurity after the failure of The Stupids. But either way, when either of these guys were at their peak, they did some truly amazing Hollywood magic:
Carpenter
The Thing
Halloween
The Fog
They Live
Escape From New York
Big Trouble in Little China
Landis
The Blues Brothers
Animal House
The Stupids
Coming to America
Trading Places
The Kentucky Fried Movie
David Lynch. Oh I love me some Lynch. Famously independent, unapologetically artistic, and more than a little self-indulgent, the patron saint of film school students Lynch is responsible for some of the most original and personal films in the last century (he gave us Twin Peaks and basically fostered the Second Golden Age of television), albeit at the cost of accessibility, but no less important as a result:
Blue Velvet
Lost Highway
Mulholland Drive
Eraserhead
The Straight Story
David Cronenberg spent most of his career giving audiences OCD with his "body horror" films that depicted the effect of human psychosis of our physical forms; lately he's branched off into more traditional fare with his sterile but poignant style but never strays too far from the beauty of human grotesquerie:
Dead Ringers
Naked Lunch
The Fly
Videodrome
Crash
A History of Violence
and finally, James Cameron and David Fincher. Since both regularly compete for the slot of "uncompromisingly intemperate perfectionist auteur" left vacant by Kubrick's death I figure they're more alike than different. Cameron favors the sterility and precision of technology and operatic action sequences while Fincher prefers the grungy industrialism of expressionism of European filmmakers, and both produce incredible works of technological precision and strong human emotion:
Cameron
Aliens
The Terminator/Terminator 2
True Lies
The Abyss
Fincher
Fight Club
Se7en
The Game
Zodiac
VERY Honorable mentions: Billy Wilder, Michel Gondry, Mark Romanek, Jim Jarmusch