(Very short) The appearance of the train carrying Strelnikov in Dr. Zhivago (just the train, not any following scene)
The last outpost where the bridge is destroyed every night and rebuilt every day in Apocolypse Now
The ending in Pan's Labyrinth
Bone becomes spaceship in 2001: A Space Odessey
"Open the pod bay door, Hal" also in Space Odessey
Bret carries Scarlet up the stairs.
"I am Spartacus!"
"You made her meow?" in When Harry Met Sally
Departing on the ghost bus in Ghost World (but you'd have to see the whole movie to appreciate it)
I suppose most people haven't seen Pan's Labyrinth. This clip of the end was all I could find. The girl has been told by Pan (whom only she sees) that she is a princess who must prove her worth to be reunited with her family. The baby is her half-sister and the daughter of the bad guy. Pan's final test is that she must turn over the baby to Pan for some evil purpose. She refuses. When she is killed she learns she passed the last test.
The background for the final scenes of Ghost World: The old man is waiting for a bus that doesn't exist. Enid has been making a mess of her own life and the life of Seymour, whom Enid met when setting him up with Dana (not in these scenes) as a prank, expecting him to be humiliated. The prank becomes a serious relationship, but Enid ruins that and causes Seymour to lose his job too.
the Shining 80 the scene with the stairs
its a Mad Mad Mad Mad World - the great chase, the scene at the big W gathering, the scene of characters pulled over at the beginning
Back To School - the scene of Rodney doing the Triple Linding, the scene of Rodney causing a scene in the classroom with professor Barbey
What always gives me chills, even just thinking about, is the scene in 2001: A Space Odyssey when the pod is leaving the mother ship and advancing toward the monolith. Hard to explain. I guess it just fits my conception of what it would be like floating in outer space. It is also strangely similar to a dream I had years before seeing the film.