Special mention should go to the earliest surviving animated feature: 1926's The Adventures of Prince Achmed.
1930s- Snow White and the Seven Dwarfs. Duh.
1940s- It's a toss-up between Fantasia and Pinocchio. Could you decide between the two?
1950s- I haven't seen Lady and the Tramp yet, so Alice in Wonderland is on top for now.
1960s- Yellow Submarine. (Honorable Mention: Rudolph the Red-Nosed Reindeer.)
1970s- Either Phantom Tollbooth, or The Mouse and His Child.
1980s- The Secret of NIMH and Who Framed Roger Rabbit?.
1990s- By this point it's hard to choose... all of Disney's films before Pocahontas are excellent, but in a way it's like apples and oranges. And so many others are worthy of mention, even some of the direct-to-video/TV ones. So who can say?
2000s- PIXAR. (Honorable Mention: Lilo & Stitch.)