This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The Last Temptation of Christ
A terrifying film in general. Throughout the movie there appear several calm moments but have an underlying sense of eeriness. However, there's several disturbing scenes.
One of them being a crucifixion scene in the beginning where a man is crucified for sedition. His screaming in the scene is just unbearable, and the look of guilt in Jesus' eyes when the blood from the man's ankles sprays on his face is just heartbreaking.
Jesus pulling his heart out. The scene is very ominously lit and has eerie yet epic music accompanying it.
Jesus healing the lepers after the aforementioned scene is made even more eerie is the music playing over the scene.
The crucifixion scene is very... eerie.
Any scene where Satan appears. It should be Nightmare Retardant, but the fact that it's just a pyro going off with an ominous British Accent makes it downright terrifying.
A bizarre thing that happens after Jesus' death.
To elaborate: the film abruptly stops and fades to white. Apparently this was not intentional; the camera failed at the exact moment Jesus expired. Rumors of Divine Intervention still linger.
In the novel: the scene where Barabbas kills the resurrected Lazarus. Barabbas, who had killed many times and had never felt any fear, ran away in horror after doing the deed, and we can see why.