The kidnapping of the slaves and the extremely traumatic stealing of their essence. I felt so much horror and pity as I watched the slave's life force being taken. And then Kira's!
This. It was almost disgustingly creepy.

Essence drain, those eyes going blank and those cute podlings going all wrinkly and stuff
Creeped me out.
Also fizzgig whats its name jumping out of the hole for the first time. Knew something was gonna pop out didnt expect it to be screaming like mad.

Collection
http://www.imdb.com/list/4zXrE3AAzT4/

The kidnapping of the slaves and the extremely traumatic stealing of their essence. I felt so much horror and pity as I watched the slave's life force being taken.
I think probably this. It's the part that stuck with me.

The death of the Skeksis Emperor, especially the way he says "mine!"

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That last line brought such laughter in the whole theatre which had been a serious movie up till that line. It was much comic relief, thanks for the flashback, yes I'm old!

thank you all for your interesting thoughts!

When I was a kid, I was sad to see Kira's mother get killed by the Garthrim. Very disturbing scene where the Garthim yanks her offscreen as her daughter watches in horror.

Positive thinking and positive action add up to results!

I only watched again recently, after many many years. I had forgotten how dark the film was in parts. Wonderful conceptual design and visuals throughout and was impressed by the film, when first released. Loved the ending shot, with the lush transformed world and the beautiful crystal palace in the background.
I think the film pushed the envelope, with what it could get away with for a "family film" and being done with puppets, it somewhat lessened the impact of the scenes. The assaultive disrobing of The Chamberlain, could be tantamount to attempted rape. It was also a shock when Kira got stabbed and died, as she was such a lovely and brave character. However, I knew that she would be brought back to life, so I wasn't that distressed.
Jen: Wings? I don't have wings!
Kira: Of course not. You're a boy.

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I've never been a squeamish kid when it came to films etc, a part of me always knew it was make believe. However, there were two scenes that always unnerved me in this film.

1. Right at the beginning, when the Skeksis drew their power from the crystal. It's just the way they stare at that thing while purple beams of light radiate from it. Always gives me the creeps.
2. When the emperor dies. Something about the way he disintegrates always disturbed me. Creepy as hell! haha

The Chamberlain disturbed me most (and especially the scene of his violent banishment) the film generally was pretty creepy, but he was by far the creepiest for my young psyche when I saw it in the theater way back when. Not sure why, but it's something about his eyes and that evil grin he has for most of the film.
I will probably get laughed at for this, but I used to sneak downstairs when I was younger (right around the time this film came out) and watch horror movies on late night TV. I saw Poltergeist, Savage Harvest, American Werewolf, and several others that way and
none
of them came close to creeping me out the way this film did.
Henson & Co. hit the nail on the head.

the eating scene, that drum stick that moved, couldn't eat chicken for a long time.