It's impossible for me to pick three, but it has always been the more sentimental scenes rather than the action/blow up stuff scenes that gets to me.
One of those scenes is when Bruce did the third climb in TDKR, and the blind man and the other inmates chanted Deshi Basara. I can't lie, tears streamed down my face when he made that jump.
That scene in TDK when he's sitting in his bat suit with the cowl in his hands, and Alfred walks up to him to give Rachel's letter is another one of those scenes.
Another beautiful scene is in BB, when Batman is climbing up a ladder and a kid tells him: "The other kids won't believe me." I kind of wished that John Blake would've turned out to be that kid. That was my first impression watching TDKR, because my mind was so set on that.
And how beautiful was this: