Al Pacino was nominated for his villain role in Warren Beatty's "Dick Tracy" in 1990, and, personally, I thought he deserved it a lot more for The Godfather, Part III. And I'm also proud to call The Godfather, Part III a great film, even if it doesn't live up to the first two.
And Adrien Brody's win over Daniel Day and others might've been for the fact that he really gave up a lot just for the role. He sold his apartment, car, and lived by only eating small food, like eggs. And of course he learned to master playing the piano.