I agree with the very first scene mentioned in this thread, Cliffhanger. I haven't watched the movie again since that first time.

I'll add any movie where someone gets the tendon at the back of their foot sliced, like in Pet Sematary.

"The choice" scene of Sophie's Choice.

Needle to the heart in Pulp Fiction.

Caché:

The ending of Chinatown.

Pan's Labyrinth - the peasant getting his face smashed in.

The opening montage of Up - damn you, Pixar, for consistently making me weep in front of small children for over a decade.

No Country for Old Men - any scene involving Anton Chigurh makes me want to crawl up under a chair and hide.

V for Vendetta - the story behind the letter that Natalie Portman finds in her prison cell is both beautiful and devastating. I've avoided watching the movie more than a couple of times because I don't want to endure that scene again.

Gets me every time. The end of It's a Wonderful Life too.

Ooo that's a good one. You can almost feel it.

Crash

While I think the opening montage to Up is quite beautiful, the scene that really gets me is near the end when Man, that's getting to me just thinking about it.

The end of Schindler's List at the grave and the sad song in Toy Story 2 are the 2 scenes that get me every time that haven't been mentioned.

Frozen



that was a pretty powerful moment

Ditto. Great movie, worth watching, but I never want to see it again.

Also, the car wreck scene in Enter the Void.

The Elephant Man-"Nothing Dies"

DAWN OF THE DEAD (1979) - the scene where the zombie husband takes a chunk out of his wife in the housing project right at the beginning. Gave me bad dreams back then and haunts me to this day. That whole scene, in fact. Brilliant, but disturbing. Yes, I know it's actors and makeup effects, but still...the illusion is very powerful.

off the top of my head right now:

The scene in 28 weeks later with the thumb eye gouging grossed me out big time. I could tolerate stuff like Fulci's Zombi eye piercing but that one just seemed too real.

and as ridiculous as it sounds, that cockroach scene in Nightmare on Elm Street 4 kind of bothers me. Ridiculous concept but so disturbing.

Same with in House of Wax cringing....

As a kid, my dad let me watch Amityville Horror (thanks for nothing, dad)... the scene where the little girl is talking about her "imaginary" friend Jodie and her mom goes to close the window only to have those two red eyes stare back at her from outside. Everytime I close a window late at night I think of those two red eyes.

Agreed, but it's really the combo of the two that has such an effect

Funny I used to watch that scene of Cliffhanger over and over.

Hachi: A Dog's Story

The ending montage of Requiem for a Dream is probably one of the most disturbing movie sequences that I've ever seen.

Transmorigification (sp?) can be a creepy subject matter. The man who did the FX for that part did a similar scene in the movie version of The Guyver (to Mark Hamill no less) and the way it occurred was disturbing. Problem is the end creature was obviously a puppet and didn't pack much of a punch.
I think the reason Cronenberg's The Fly is so effective is because they make the creature very believable and really fuel the transformation's impact.

I initially found the soldiers being turned into pigs in Willow disturbing, but with time kind of found it a lazy excuse to create another obstacle for the hero. The make up hasn't aged too well either.

Screaming Mad George, a Japanese guy who was in a band before that if I remember. Things about that scene look a bit cheesy of course but it's definitely gross out how her arms snap off and the whole face peeling back part.

Any time those two hip hop robots talk in Transformers 2. Nightmares I tell you.

In recent years there has been a couple.

The Wrestler


Wall-e


Silent Running (Not so recent)

Anything to do with animals gets me. Kill a woman, I'm cool with it. Kill a child, no problem. Kill a dog and I lose it.

^that...and any of those "Now go!" scenes where the dog's owner needs the dog to leave him for some reason so he acts mean to it to get it to stop following him. Even though those scenes are cliched, they get me every single time...I hate watching them.