The immediate effects on Logan after surviving the Nagasaki atomic blast.
You will wince in horror multiple times in the Self-Surgery scene.
The moment Viper sheds her skin is rather creepy.
The Silver Samurai drilling into Logan's broken claws' marrow and sapping out his Healing Factor. The fluctuation of the healing ability on both of them during the procedure and the fact that it's the closest moment Logan has ever been to dying are quite nightmarish.
The actual nightmares Logan suffers with Jean Grey.
The ninjas ground into meat and blood by Yukio. The sounds and the blood spraying onto houses lining the street...ugh!