I don't know. Part of it might just be Cillian Murphy bias. I like that guy a lot. The rest of it, well, I think the fight between Batman and the Joker is great, where he fights off the dogs and then pins the Joker as he is about to detonate the boats... But something about the scene where Batman is gassed, ignited and shoved out a window by some random crazy doctor just impresses me. I guess it's partly expectation. My limited Batman knowledge 'expects' the Joker to gain the upper hand on Batman often: he's his ultimate foil, whereas I never really knew much about the Scarecrow so when he got the edge on Batman, it was neat, and unexpected. (As an aside, I also love the scene where Crane is dosed with his own fear drug and all he can manage to say is "Dr Crane is unavailable at the moment, but if you'd like to leave a message...")
Don't get me wrong, it's hard for me to say Begins edges out the Dark Knight. In fact, I may not actually go that far: I was totally engrossed by the Dark Knight's story. Plus, Two-Face, in addition to Ledger's amazing performance, Eckhart had a great turn. And there's that scene where the Joker's stumbling down the road with the machine gun... I do love that. Mm. Maybe I'll rewatch those movies today.
But yes. I would have to go "fire out a window" over "Boat scene". I'm sorry
There is no denying that.