By uncanny I essentially mean the sort of subtle off-base emotional discomfort you feel while watching Eraserhead or The Shining for example.
Extending the question, sometimes single scenes with slightly more intense or completely different qualities to the rest of the movie can 'make' the movie. Everything during and after Laura and Ronette are dragged to the train car in the ending of Twin Peaks: Fire Walk With Me, or the sitcom scene of Mallory's home situation in Natural Born Killers.
Not outright horror necessarily, but hitting on those discordant subliminal notes to put you on edge, building to horror or further tension.