Did everyone but me forget about not only the guy with the live bomb inside of him which from start to finish was terrifying, but also the episode where Bailey is operating on a patient and she wakes up? The poor woman was scared to death and freaking out any time Bailey went near her, and you could tell it affected her too.
That episode when Dr. Shepherd, Sloan, et al. need to split a teenager's lower face so they can access a large bony tumor located at the base of the kid's skull and upper spinal chord. Even Callie is disturbed by how much pain would be caused by breaking the jaw, which is only part of the horrific procedure. Meredith calls it decapitation.
Cristina's description of her, Meredith, Derek, Mark and Arizona's time in the woods especially the part about the animals fighting over Lexie's corpseshudder
Christina describing the death of her father to Hunt, her trying to hold his chest closed to slow the bleeding and she felt the moment he died when his heart stopped and she was only nine when it happened.