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Oohh, Memento and Dark Knight are tied right now. Just as I expected. I've seen The Dark Knight about 10 times and I still think it holds up well. I do think that there were more anti climaxes than there should have been but that's minor criticism compared to just how well it's made. Every other aspect is just spot on for me.
The Prestige is slightly just behind Dark Knight for me, as fantastic as that film is. I'm gonna have to think long and hard about this poll because with the exception of Memento and Batman Begins i'm not 100% sure where his films fit as far as a best to 'worst' list goes.
Following would be after The Prestige, I think.