I
replied to this a long time a long time ago, but I have some more to add, some of which have already been said by other people.
Spoiler warnings for all, movie titles in bold so you can glance at any to avoid.
Collateral - the scene with the coyotes crossing the street with Audioslave - Shadow on the Sun softly coming in to the background. The expressions on their faces are perfect as is their silence throught this and the next minute or so. I often put the DVD in just to watch this one scene.
Apollo 13 - the countdown and launch, very powerful scene, another that I can watch indpendent of the rest of the film. Even with a few (small) parts of the special effects starting to show their time, the way it is filmed is perfect. I love the "go / no-go" check in mission control right beforehand just as much also.
Garden State - the party scene where he just sits there while everything else is going on around him.
The Great Escape - When they found Tom, also when they line everyone up in the field near the end
The Godfather - When Michael is planning out the killing of the police captain in the family office. It shows him starting to take on the mantle of his old man despite his brother technically being in charge of everything. Also, when Don Corleone finally asks the undertaker for his favor.
Closer - the scene in the strip club. And not just because its Natalie Portman stripping (doesn't hurt), but the dialogue and acting is perfect for that scene, especially after you see the end of the film
Bad Santa - "I beat the shit out of some kids today ... It made me feel good about myself." Also, the "fuck me Santa!" scene.
Children of Dune - eh, its a miniseries, but close enough. The ending of part one (which covered the Dune: Messiah book) with the montage showing the settling of the affairs with the song in the background (Inama Shurif). Also, the scene in part 3 where he finally gets a chance to talk to his father while sitting on the dune
Return of the King - as someone else said, the lighting of the beacons scene. beautifully made.
The Two Towers - When Treebeard sees the destruction and yells out and all the other Ents come out of the forest for their last march and the assault on Isengard. The music there is perfect as well.
Leon: The Professional - also one someone else said, when Gary Oldman asks for everyone and, when questioned about it, screams "EVVVERRRYYYYONNNNNEEE!" Immediately followed by the countless police cars screaming in from every direction.
Damn I have a lot of favorite scenes.