I've several:
Batman Begins: The 1st scene where Ra's is training Bruce - a la - 'You know how to fight six men; we can teach you to engage six hundred.' [That entire sequence was well done]
The last conversation between Gordon and Batman:
Det: I never said thank you.
Batman: . . .and you'll never have to. *jumps off of building*
^That's my favorite ending to a superhero film.
Superman Returns: The entire plane sequence, esp. when Supes is flying to the head of the aircraft to stop it.
- AICN had a very interesting take on that scene, and it kind of added another dimension to it. The review asked the reader to imagine being Bruce Wayne or another hero within that universe watching Superman physically will the plane to safety. I know it's a bit much, but I liked the thought of it.
X2: The verbal exchange between Stryker and Senator Kelly(Mystique) where Logan's engineer explains that he had been running black-op missions while Kelly was sucking on his mama's teat at woodstock.
Spider-Man: I like the 'dual fates' shot of Spider-man's eyes when he had to choose between saving MJ and/or the young hostages.
V for Vendetta: The first time V and Evey meet was a magnetic interaction for me; I didn't like the alterations / deviations from the written material, but I loved Hugo Weaving's performance.
Superman The Movie: The Jonathan Kent 'you're here for a reason speech.'
also Perry White's: "Now look. The Post: "It Flies." The News: "Look, Ma, No Wires." The Times: "Blue Bomb Buzzes Metropolis." The Planet. We're sitting on top of the story of the century here! I want the name of this flying whatchamacallit to go with the Daily Planet like bacon and eggs, franks and beans, death and taxes, politics and corruption."