This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Men in Black
The alien at the beginning of the first Men in Black film freaking out when the police officer sees him.
Kay decides to get his gun back after the bug swallows it...by getting the bug to swallow him.
The infamous Balloon Belly scene from the opening of the second film. Silly? Oh yes. But now take a moment to imagine not only being swallowed alive, but crushed down to not even half your size in the process. Let's be thankful this happened to a would-be rapist of all people.
The poor guy's "Hey what the-" followed by his scream of terror didn't help.
Some of the alien designs can, in general, be rather unsettling, especially when they look more only slightly inhuman shaped, or are shedding a human disguise.
Boris has tiny, knife like killer parasites, murders his girlfriend for no reason at all, and can erase you from time.
Edgar's skin, decaying throughout the film, is arguably more unsettling than his real form.
And speaking of skin, the idea that he skinned the poor guy alive with his bare hands.
The scene where his victim's wife comments on the looseness of his skin, and he stretches his face back against his skull.
"There. Izzat better?"
One minor one from the film's novelization; when going to Jeebs' pawnshop, the future Agent J warns Agent K about how his car is likely to get stolen. K brushes it off, and mental dialogue reveals why he's so nonchalant; his security system is alien design. What does it do? It quietly and casually disintegrates anyone who tries to pick the lock! By the time that they step through the shop's doors, about five would-be carlifters are dead, and K just smirks to himself that this neighborhood is going to get safer and safer the longer they take inside.