The Giant Warrior◊ in the movie. It gets worse when it begins rotting away and the flesh literally pours off and exposes the bones and skull. To top it off, it shoots once, creating something resembling a nuclear bomb going off.
When Nausicaä burns her foot (the one with the open wound) in the Acid Lake, her scream (in either the Japanese or the English dub) is very wrenching.
The whole "seeing dead people going into the light while a childish voice sings a disturbing song" is rather unnerving.
Seeing the young Ohmu used as bait is both horrifying and a Tearjerker at the same time.
The Ohmu, period. Despite the appearance of a baby version of them in the end, colossal insect monsters with multiple red eyes mindlessly charging and killing themselves in suicide attacks on cities aren't exactly soothing. It's probably this very intimidation factor that has kept mankind from realizing they're sentient for so long.
Nausicaä's dream in which she remembered trying to keep an Ohm as a pet, having it taken away and pleading for it not to be killed was both this and tear jerkingly sad.
When Nausicaä and Asbel discover the eradicated city of Pejite, with thousands of dead insects everywhere alongside the occasional human body, and a few dead Ohmu stranded in the city.
Nausicaä going into a berserker state against the Tolmekians who kill her father. Up to this part of the movie, she has been kind and gentle and to see her act like this is really kind of scary. Actually, ANY time she shows actual anger.
Nausicaä's reaction doesn't help either. In fact, the only thing that snaps her out of the frenzy is Lord Yupa deliberately intercepting her attempt to impale a Tolmekian... by getting himself stabbed.
Some of the insect designs in both manga and movie are really creepy, particularly the flying ringworm thing◊.
The Emperor's flashbacks to his father's death by plastic surgery. As if it wasn't enough to see his father's skin tear open and his organs spill everywhere, he was a child at the time.
Nearly everything involving the Holy Crypt of Shuwa. The dark, organic imagery and the Heart of the Crypt itself are utterly wrong and alien...