The opening sequence of the spacecraft literally being swallowed up by the larger spacecraft. While we're later shown that the craft immediately returns to Earth, and both the Russian cosmonauts and an American astronaut are alive and being held in a cell (from where Bond frees them), the spacecraft from the opening sequence had an astronaut on a lifeline that was cut when the spacecraft was being swallowed up, leaving him to freeze and suffocate to death helplessly in outer space.
While looking through the documentation taken from Osato's safe they find a photo of an oil tanker that was taken by a tourist, later killed as a "routine precaution". Imagine been assassinated for simply taking holiday pictures. Even Bond seems somewhat disturbed.
Blofeld punishes Helga Brandt by dropping her into a pool of pirahnas. We've already seen them strip a leg of lamb to the bone in seconds; now we see Brandt burst to the surface, scream and try to get to shore before she's dragged underneath again. What makes it worse is that we never see what's down there. Traumatizing.
"KILL BOND, NOW!"
Aki's death. Think of how many times you've swallowed in your sleep or slept with your mouth open. Pleasant dreams.
The poison was meant for Bond, and she accidentally drank it.
Blofeld's appearance is well known today, but his introduction can be unsettling to the rest with the way he quickly looks at Bond with his wide, scarred eyes.
The Garden of Death, which really lives up to its name. At one point Bond sees one of its suicidal visitors with his head grotesquely swollen from the many poisons that the place harbours running into a pond, only to be eaten by hungry piranha inhabiting it.