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Nightmare Fuel: The Amazing Spider-Man
The First Film
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 bit 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 Conners responds in a deep, growling tone:
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.
Guessing this an Adult Fear, but Aunt May has to deal with Peter going out on all hours and returning with bruises and claw marks.
The bridge scene, with all of the panicked citizens running from The Lizard. Then there's the child that Spider Man had to save... it was scary to almost see that child die.
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 Video Game
The cross species rampage at the begining.
The cross species virus, any direct contact with them (espically Vermin) will result in infection, infection leads to death, or becoming one yourself.
The fact Iguana has telepathic control over those infected by the virus.
Smythe sending his entire robot fleet onto the city during the climax.
Peter watching Connors turn back into the Lizard as he begins to pass out.