This is a good question. I was just thinking of posting this poll the other day. While all three films are excellent, there is one I favor the most when I watch it. When Batman Begins was released in 2005, I thought it was awesome, but I still favored Burton's 89' Batman over Begins--mainly because The Joker was my favorite villain, and 'Begins' lacked a certain theatrical villain punch, so to speak.
Then The Dark Knight came out, and to me, that was THE greatest batman movie ever. Several years after TDK hype simmered down. I watched both movies again. While the performances (most identifiably, Ledger's) in TDK are superior to any comic book movie ever produced, I for some reason, fell in love with 'Batman Begins'. I just saw 'The Dark Knight Rises' a couple of nights ago, and all it did was remind me of how perfect 'Batman Begins' really was. Without those sequels, it's predecessor would not feel as complete. Having seen all three films, each one is unique in some way; 'Begins' had a brilliant story arc, Dark Knight had Oscar winning performances, and 'Rises' had a little of both, but I feel 'Rises' will mostly be remembered for it's sensational climax--more or less, the 'Jedi' of the Nolan Batman trilogy. And yes, if we're going to compare, I suppose The Dark Knight is the 'Empire' of the original Star Wars trilogy, but seriously...
...doesn't that finale make you want to relive the journey all over again? Of course it does. Which brings us back to:
BATMAN BEGINS