This is tough: I never realized how many of my favorite movies didn't win academy awards. I'm also going to try to avoid picking any movies that I picked in the previous movie draft.
Anyway, with the first overall pick, I'm selecting Peter Jackson, 2003, Best Director, for Lord of the Rings, Return of the King. While I wouldn't count this as the best film ever, it is, in my opinion, one of the greatest acheivements in filmmaking, and Peter Jackson deserves more credit than anyone else for making that happen. Even though the award was officially for Return of the King, it was really for the entire trilogy. He and his two writing partners took an unwieldy and difficult novel, crafted it into a trilogy of films that exceeds the vision of the book. They made hard decisions in throwing out some popular characters and story arcs and preserved the best elements, and weave together the different arcs in a manner very different from the books. The decision to start Return of the King with Smeagol's backstory, for example, was a brilliant idea that gives Smeagol's story arc much greater weight in this movie than it otherwise would have had.
Though the movie obviously required a great deal of special effects, Jackson also insisted on using traditional methods whenever possible, insisting on filming on location rather than green-screening whenever they could, and having elaborate miniatures made rather than simply relying on computer models. Even the diminutive hobbits were done with stand-ins and camera trickery such as forced perspective whenever possible.
Jackson has a great sense of how to construct the story and shots in such a way of always helping the viewer figure out how everything works together, and nowhere in the trilogy is this more evident than in Return of the King, where Jackson's narrative follows a dozen characters scattered amongst four different locations and story arcs. And there are scenes in this movie such as the lighting of the watchtowers that bring tears to my eyes simply because they're such beautiful sequences. (Although, I'm an admitted wuss and tear up at all sorts of crap that wouldn't move most people.)
He's also very good about knowing when to let the music and sound and effects fade away and focus in tight on an actor's face; given the large cast it's difficult to develop all the characters fully, but Jackson does a great job of developing them by putting new characters in contrast with more established ones. As me, the most interesting characters are the three rulers - John Noble as Denethor, Viggo Mortensen as Aragorn, and Bernard Hill as Theoden - and even though these three characters have very little screen time together, he's able to find the commonalities and contrasts between them to develop all of them more fully.
He did a brilliant balancing job throughout: balancing traditional film-making techniques with advanced CGI; balancing fidelity to the original work and the demands of die-hard fans with the needs of the movie format and a typical theater audience; balancing the needs of the movie as the end of a massive 11 hour trilogy with making a movie that can also be watched on its own and weighed on its own merits; balancing a war and adventure story with the characters that drive the story. Yup, I feel pretty good about this choice as a first overall pick; I know LoTR has its share of detractors, but Jackson's work on it deserved to be mentioned among the very best of the best in terms of feats of filmmaking.