A movie I thought was mediocre the first time I saw it, but has really stood the test of time, mostly because of its nonlinear structure. No matter how many times you see it, you can never really predict what scene is going to come next. Plus, it has so much to say about the human spiritual experience.
http://www.youtube.com/watch?v=uw63_YyNsF4PS: I also really enjoyed "The Unbearable Lightness of Being" but I thought that movie was a masterpiece the first time I saw it, so for me it doesn't qualify.