From the The Color Purple:
The scene where the Danny Glover character separates Celie and Nellie and the scene in the end where the sisters finally reunite.
I really like the nightmare sequence in Vertigo.
Notting Hill, the *Ain’t No Sunshine When She’s Gone * sequence, where Hugh Grant walks through the neighborhood and all around him time moves on. Everything changes, including the seasons, but he just keeps walking. I bought the DVD just for this scene.
Jurassic Park : the brontosaurus scene. Absolutely beautiful.
Conact : “They should have sent a poet.”
Also, the scene on the Washington Mall in Forrest Gump.
In the Company of Men
The scene where the jerk reveals to the deaf woman that she’s just a victim of his gag. It was heart-wrenching.
Vampire’s Kiss
Nicolas Cage is on the brink of insanity, and is continually abusing his secretary. In one scene, he recites the alphabet in a manner that is absolutely chilling. My favorite scene ever.
The scene in Reds when Diane Keaton goes down to meet a sick Warren Beatty coming in on the train: She doesn’t see him, runs throught the station looking for him, sees a sheet covered body being carried on a stretcher, gasps and closes her eyes, turns away, opens her eyes and sees Warren just standing looking at her. Rather than run to him, she just calmly walks and he takes her in his arms
The scene in Top Gun where images of jet fighters were shot to “Danger Zone.” It was an incredible marriage of sound and sight. In the theatre you could feel the reverberations of the planes. I defy anyone to watch that scene and not want to become a pilot. Or fuck one. 
I thought the scene in “Unfaithful” where Diane Lane is on the train home and reacting to her recent infidelity, laughing one second and weeping the next, was Oscar worthy.
The last scene in “Sixth Sense” where you see Bruce Willis’ wife reach for a sweater and then you see her breath and then it slowly dawns on you…great movie.
The first one I thought of is the opening scene of X Man 2 when Nightcrawler is bamfing his way through the White House. I was so amazed that technology has finally caught up to comics. If a blue skinned, teleporting guy with a funny tail were to appear/disappear through the White House - it would look just like that.
Also from X-Men 2: Magneto’s prison break.
Agreed. I rewatch the movie just to see that scene (well, I liked the entire movie, but that scene is amazing. And the song!)
And agreed on the Color Purple. The scene where they separate the sisters is absolutely breathtaking (I think I had a thread on this a while ago, now that I think about it - Most Powerful Scenes in Film, or something.)
And the scene where they put Norma Rae into the police car.
It only works once, but the now-famous ‘chestburster’ sequence in Alien was as stunning as a sledgehammer to the forehead the first time I saw it. It also made the rest of the movie terrifying, because you knew anything could happen at any moment.
The ‘Valkyries’ helicopter attack in Apocalypse Now was incredible.
The scene at the end of Big Fish had me weeping.
And for well done scenes with a creepiness factor:
The opening sequences for The Ring and Scary Movie.
Now Sci-Fi:
Bladerunner, the REAL version WITH the voiceover, had a couple of very well done scenes. Removing the voiceover drops them down to just another plot point. The scene where Deckard wastes the pretty snake charmer skin job. “Why did I feel like I just shot a girl in the back…?” And the earlier meeting with the police chief. “He was the kind of guy who would’ve called Blacks niggers.” These scenes set and carried a mood and tone soley because of the voiceover narration. Without the VO, it’s just one more scene.
The Day the Earth Stood Still - when we first meet the alien on the White House lawn. Cheesy by today’s standards? Quite frankly, I still think it works.
Planet of the Apes - chasing Taylor. The various monkey type noises, some by musical score, others as sound effects for the extras, ending up with Heston’s best line ever. And the music for the forbidden zone, both at the beginning of the movie when they are crossing it as astronauts, and at the climax. Musical cues for visual shifts. Awesome.
I have never seen a movie that had as many moments of sheer jaw-dropping spectacle as Return of the King. But my favorite moment of all was simple dialogue, with no effects at all. Gandalf describing the afterlife to Pippin. My God, that was beautiful.
And nobody has mentioned the chariot race from Ben-Hur? (Anticipating the inevitable question, I refer to the 1959 version)
Every moment of F. Murray Abraham’s performance in Amadeus leaves me in awe.
It’s an impecable copy of the real VLA control room. I thought they’d actually filmed on location when I first saw Contact. 
This one is an amazingly well-done scene that is a reference to another amazingly well-done scene. In Farscape: The Peacekeeper Wars:
When Crichton came upon Harvey in the white room from 2001, complete with Monolith, I was dying. A brilliant homage, and beautifully done. Something in there about Crichton’s identity and destiny, too, I imagine.
I know some people have already mentioned Return of the King, but the one seen that actually did take my breath away from that movie was when the Riders of Rohan came upon the Pelennor fields. The scene with the vast cavalry of Rohan stretched off into the horizon, with the rising sun in the distance causing their armour and weapons to shine, just absolutely blew me away.
Also, in Whale Rider, at the ending when the village decides to call it in from helping the beached whales, and suddenly they realize that the young girl (I can’t remember her name in the movie) is not with them, then she is shown riding the whale, looking back to see if her grandfather can see her. The image was perfect, the dialogue was perfect, and it made me bawl my eyes out. Also, the part where she is giving the speech at the school assembly and sees that her grandfather isn’t there (whom the speech was meant for), and starts to break down. Had to remember to breathe there.
Spoilers for The Slayers, just in case…
Lina gets blasted through the stomach (ouch!) by a powerful spell, and her companion Gourry, thinking that Lina has died, FREAKS OUT.
This wasn’t my first anime, but it was probably the first time I had ever heard such emotionally powerful voice acting, and it blew me away.
Huh…seems like there’d be at least one, but I can’t think of any. The over dose scene from Pulp Fiction might rank up there. If the written word counts, then the scene where the message from the Archchancelor of the UU is read in Going Postal was pretty great—a brilliant mix of comedy, suspense, and drama.
Eternal Sunshine of the Spotless Mind:
When Kirsten Dunst is told that she had previously had an affair with the doctor and had the memory wiped from her mind. The look of horror on her face was PRICELESS. I always thought she was good, but that was GREAT.
Oh, agreed entirely – that was amazing. I bawled right through it. (And I was thrilled to hear the “far green country under a swift sunrise” line in the film; it’s my favorite in the book, but I didn’t expect it would work its way into the dialogue.)
I also want to put in a good word for the Non nobis sequence in Branagh’s Henry V, which is just stunning.
I voted on the Color Purple in the other thread too, TellMeI’mNotCrazy. The scene you mentioned was good, but the one that always stood out for me was Celie shaving Albert on the porch, and Shug [being down the street] realizing what she was about to do. Cutting back and forth between Celie moving closer to Albert’s throat with the freshly sharpened razor, and Shug running toward the house as fast as possible… man. I was literally holding my breath the first time I saw that, and I knew what was going to happen! I had read the damn book, and I still fell for it. People can say what they will about Spielberg, but he knows how to grab you and pull you in for the ride.