Since some people have included scenes that were a mix of CG and live action, I have to nominate the first full appearance of the T.rex in Jurassic Park and I also have to say that it still boggles my mind that there is a mix of CG and puppetry in the “Raptors in the kitchen” scene from JP sometimes without cutting away; I have tried and tried and cannot tell when it’s CG and when it’s puppetry.
Mine’s odd, I’ll admit it.
The opening scene of “The Rescuers Down Under.” The camera is zooming low over a, well, prairie? type environment and the plants are whipping by and there’s some very compelling music. I can’t remember it well, but I remember being impressed with that animation. Things sure have changed, huh?
Oh, and another scene in that movie when the boy character is riding on the eagle. The camera perspective is above them, and suddenly the ground drops away. My niece yelped, and she was always a very VERY quiet child at the movies.
I’m surprised I’m the first to mention it: the anime backstory sequence of O-Ren Ishiii in KILL BILL VOL. 1. Graphic, brutal, striking and compelling.
Menocchio beat me to SAMURAI JACK, dammit. I also liked the episode where Jack remembers his childhood in three separate mini-stories and the unexpected homage to LONE WOLF AND CUB in the second; and the episode with the princess and the bounty hunters that was very reminiscent of the opening railroad “wait” scene in ONCE UPON A TIME IN THE WEST.
The BATMAN: THE ANIMATED SERIES episodes that first featured a supermorphing and dangerous Clayface, and the one where the three kids imagine Batman in three incarnations, including his 40s style and the dystopian Batman from DARK KNIGHT RETURNS. That whole episode was a loving lapdance to my inner fanboy.
AHA’s “Take On Me.” My favorite animated video ever.
The silent AEON FLUX shorts on MTV. The visuals were just bizarre and sadmasochistically kinky. Once they insisted on voice actors and dialogue for the extended episodes it ruined the series for me.
The faintly jingoistic “Shot Heard 'Round The World” from SCHOOLHOUSE ROCK. The perfect marriage of lyrics and visuals. Edges out “No More King” and even the beloved, “I’m Just A Bill.”
For me, it’s the way Studio Ghibili is able to do wind. Somehow, in all their flying scenes, everything, big or small, moves in just the right way that you can feel the air flowing around the screen.
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Most of Laputa
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The scene in Spirited Away as Haku flies up in front of the balcony where Chihiro is standing, followed by the paper wasps chasing after him
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The catbus
Another vote for the motorcycle gang fight in Akira. Now, it’s just kind of “hey, that’s something,” but at the time it was just astounding.
In Sky Captain and the World of Tomorrow, pretty much every single scene was amazing, so I won’t even bother trying to pick a single one out.
Pom Poko is my favorite of the Studio Ghibli movies and has tons of sequences that stand out either because they’re so moving or because they’re so cleverly animated. The tanuki’s parade in the city, the sequence where all the tanuki are practicing their transformations, and the bit at the end when the main character runs to a party in the clearing, transforming from a harried businessman into a tanuki as he runs.
The first “tree-surfing” sequence in Disney’s Tarzan was incredible at the time.
The Incredibles was full of 'em – the door sequence with Elastigirl that Miller already mentioned, was just perfectly paced. Even just the lava wall opening and closing was a cool sequence.
Both the train race finale at the end of The Wrong Trousers, or the whole chase sequence at the end of A Close Shave (especially when Wallace orders the sheep to “get organized”), had me as close to jumping up and down and cheering as I’ve ever been in a movie theater.
If I had to pick one most striking, I guess it’d be the scene where Eddie Valiant drives through the tunnel into Toontown in Who Framed Roger Rabbit?. Thinking about it, it was probably one of the easiest sequences in the whole movie to do, but it was perfectly timed and perfectly conveyed the sense of, “okay, something really special is about to happen.”
The last ten minutes of the final episode of Cowboy Bebop* are pretty stunning. It’s not just the animation, it’s animation+music+content+the little quote at the end (instead of “See You, Space Cowboy”) that suddenly throws the entire series into perspective. But in any case it’s very striking.
The opening / teaser trailer scene, of Disney’s Dinosaur.
I’ll throw a little love TV’s way.
Duck Tales - The show just had the perfect look, which it naturall inherited from the comic book but still the show just looked amazing. Particularly the gold fever episode where the temple was collapsing into the molten gold below and they were all running for their lives.
Futurama- It just had some amazing 3-D shots where the animation was just moving so fluidly. Like the battle scene between Earth and Omicron Persiei 8. And the detail in some scenes like the robot party Nixon throws in the Galapagos.
back to movies
Aladdin, when he was riding the carpet while trying to escape the Cave of Wonders. As the carpet twisted and dove down to avoid the wall, it felt like I was on a roller coaster ride. I had never felt that from animation before.
In the early 80s I was often enchanted by the Edward Goreyesque animation on PBS’ Mystery! series.
Mine is somewhat weird and obscure, but I have always had a huge spot in my heart for Rock & Rule… especially the Uncle Mikey Show.
Most of what’s been mentioned is computer generated, or at least partially so. In the '70s when all animation was hand drawn, Fantastic Planet took my breath away. The art work was by Peter Maxx (I think) It wasn’t that any thing appeared real, in fact that was the draw, nothing looked real. It was an Acid Trip come to the screen.
Wow man. 
The battle scene in the End of Evangelion movie where Asuka goes bersker on the mass production Eva unit. That has to be the single bet giant robot combat scene drawn by the hands of man.
In Kiki’s Delivery Service, some of the flying scenes are pretty cool.
yes, Kiki’s Delivery Service. it’s not striking and mind-blowing per se, but it is magical.
In a CGI fashion rather than ‘animation’ per se, I vote hands down for the scene in LoTR III where the dead army ride out… sheer goosebumps moment.
And as for real animation, I was completely blown away by Final Fantasy (the movie) and found it very easy to forget for a while that the characters were not played by real humans. Of course, that’s not a scene, it’s the whole deal.
Another one:
The scene in Mulan where the Huns are riding into the valley. It’s absolutely stunning.
Not exactly animation, but a video game. But hey, we can all agree they’re art forms, too…right?
Spoilers if you haven’t beaten The Wind Waker.
The final battle where Gannondorf loses his chance at touching the Triforce. He begins laughing maniacally, not answering any calls until Zelda picks up Link’s sword, says “What are you laughing at? You’ve gone insane.” On cue, the ocean starts falling down above them, leaving a small arena where Link and Zelda stand. Gannondorf pulls out his swords, grins disturbingly at Link, busts through the water, and attacks. Probably the single most artistic moment I’ve witnessed in a game.
Not my favorite, but certainly the two most striking I’ve ever seen.
Hmmm. Let’s back down a little.
There have been many much better since then, but it blew me away at the time. Now, I’m a bit more jaded and flashy animations for their owns sake is lost on me.
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Beauty and the Beast. The Ballroom Dance with Belle and the Beast. I know they used computers to coordinate it, but the way the “camera” swoops and is part of the dance, the way the floor tiles gleam… I think it was the first time we got a glimpse of what you could do, not only with animated characters, but with an “animated camera”, i.e. one that’s not fixed on a tripod or dolly.
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Circle of Life from Lion King. Agaqin, it’s the virtual camera that does it for me, how they change focus from small insects on a leaf to large animals on the turf. Another example of Disney animating as if it was a real live camera.
[aside]
I just got Aladdin on DVD and how could Disney ever lose the edge they had ten years ago? Mermaid, Aladdin, Lion King, Beauty and the Beast. They got a "BEst Movie nomination for B&B (first time ever for animated film) and didn’t pick up on that… Sheesh.
It went assembly line after that. “A new, big family feature out every year, let’s form a comittee and try to decide what story to exploit next…”
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Not only did you steal my show, but you nailed the exact episode as well.