For those who are arachnophobes, the scene where Peter first steps into the room in Oscorp with all of the spiders and accidentally activates something that ends up dropping several spiders all over him. Even scarier knowing that one of those spiders later bites him and then was eventually found to still be crawling around on him. Not to mention all the closeup photos of big hairy spiders during Peter's internet research. And the pictures of spider bites.
The lizard-mouse's ultimate form. We see it, half-lizard, eating its fellow mouse and twice its original size, with the hind legs and mouth of a lizard.
The Lizard himself is quite scary. A noteworthy moment being when a transforming Connors enters a taxi to head for the same place as the Oscorp agent and the driver asks if he's alright, to which Connors responds in a deep, growling tone:
Perhaps the creepiest by the Lizard is when he confronts Peter at his own high school.
"Nowhere to hide, Peter!"
What makes it creepy is just how.... "normal" it sounds. No real baritones or growling. It sounds almost completely like it's pre-transformation Curt Connors speaking. This vocal dissonance plus the Slasher Smile he's wearing as he says it in that playfully mocking tone just makes it all the more unnerving.
The scene in which Peter has spun a web to see if he could track the Lizard in the sewers. We see a huge shadow, thinking it's the Lizard, when it turns out to be just a common lizard. Then we see a larger tail drop behind Peter...
When Gwen is hiding in the closet from The Lizard. The Scare Chord does not help matters.
The bridge scene, with all of the panicked citizens from The Lizard. Then there's the child that Spider Man has to save... it is scary to almost see that child die. It also shows that these are normal who are being affected by the events of the movie. Unlike in most other Spider-Man media, we see these events as actual tragedies rather then just Fan Wank moments of awesome action. It's also the first time we, albeit subtly, get an insight into Peter's relation with the normal everyday citizens of New York, and his feelings about saving normal strangers lives.
In the deleted scenes, there is a sequence that ends with the death of Dr. Ratha in which the Lizard is implied to bite his head off.
The Cross Species Rampage at the beginning of the game, with Scorpion, Rhino, Nattie, Vermin and Iguana attacking the Oscorp scientists. Doesn't help that as the rampage starts, Vermin bites Gwen's arm in front of Peter. Each cross species in fact has their own moment:
Iguana slowly prowling like a Komodo Dragon toward a helpless scientist, drooling and snarling as the scientist frantically backs away and pleads for his life. One can only imagine his fear as he hopes to whatever higher power he worships that it has a shred of humanity and just might spare him if he tries to reason with it, and then the realization that it's nothing but a mindless animal that sees you as prey and nothing more.
A panicking employee running down a long hallway and into a storage area, trying to close the automatic door. Just as the door closes, Rhino comes barreling down the hallway and forces the door back open long enough to slip inside and trap the man in the room with him.
The cross species virus itself, Smythe sums it up best.
Smythe: Any direct contact with these things lead to infection; infection leads to death, or becoming a cross species yourself.
The Infected, which are basically humans taken into the sewers, becoming zombie-like animalistic creatures. Turns to Fridge Horror when you realize that these are probably innocent people with their lives ahead of them.
During the climax, we see New York is basically a warzone; people are walking around, likely on the verse of transformation, and the infected are loose on the streets to, but are restrained by metal fences from attacking Spider-Man, and there are Smythe's robots going rampant, set to kill the infected citizens, and Smythe personally operating a giant robot that is constantly firing missiles. Basically it's like the end of days.