Just the entirety of that specific scene, which is basically Otto's Diabolus ex Machina and perhaps the single most intense scene in the entire trilogy. He had just discovered a scientific breakthrough with his reactor...and then, the magnetism kicks in. Thinking it'd eventually stabilize, things rapidly go to hell as the reactor goes totally bonkers. Spider-Man tries to unplug the reactor, but Otto refuses, still believing that he still has everything under control. And then Rosie dies right behind Otto (see below), he gets electrocuted (see above), and then Spidey finally shuts the thing down, causing it to implode. And thus began Doctor Octopus' legacy...
Though the Bloodless Carnage mitigate the scene a bit, but still unsettling and disturbing for some people. It might even make it worse!
The scariest part? Otto was unconscious. His tentacles did that all on their own. Imagine waking up after a horrible accident, only to find yourself in a hospital with everyone in the room dead. You begin to hear a voice. Four, in fact, each one of them telling you to do horrible things. The look on Otto's face when the tentacles remove his blindfold and rouse him is one of horror as he wakes up to a room full of corpses.
The entire scene is horrifying, but one of the more notable features is that there is absolutely no music playing. The rest of the film has a bombastic and grandiose score but in this one scene the only sounds are those of the doctors' blood-curdling screams while they're being murdered.
It's really a scene straight out of a horror movie. The Evil Dead movies, to be exact. Raimi used his experience on those films to great effect, cutting quickly between pieces in his Signature Style, proving he can make a downright terrifying sequence even with absolutely zero blood.
After retiring Spider-Man, Peter sees a burning building and can't bring himself to do nothing. He rushes in to try and rescue a stranded kid on the second floor. What's really shocking is that you'd expect this moment to showcase how Peter's resolve can compensate for his fluctuating spider-powers, but it doesn't. Peter nearly got himself killed along with the little girl he tried to save, surviving on pure luck. Afterwards, the rescue team mentioned that there was still one fatality.
Ock kidnapping Mary-Jane and his threat to Peter about her. The Slasher Smile as he grabs MJ and makes his exit just seals it.
Doc Ock: I want you to find your friend Spider-Man. Tell him to meet me at the Westside Tower at three o'clock.
Peter: I don't know where he is.
Otto calmly takes off his goggles and looks Peter in the eye.
Doc Ock: Find him. (two tentacles rise up behind Mary-Jane, shrieking) Or I'll peel the flesh off her bones (tentacle snaps menacingly)
The loud stomps of Doc Ock as he climbs up to Harry's balcony to confront him. Roger Ebert referred to the tentacles scaling a building sounding like "the drums of hell".
Harry hearing the Goblin laughter just before he starts hallucinating Norman's reflection in the mirror.
The Video Game
From the PC version of the game, New York is turned into floating islands, courtesy of Mysterio. In the first part, the floating islands are only several hundreds metres or so above the ground. In the second part, the floating islands are located very close with the earth's atmosphere, where many meteors hit and the ground can be barely seen. In the third part, the floating islands are in outer space.