In this game, if the player goes to the Chrysler Building, there are feathers on one side of its upper level. These feathers are left over from Spider-Man's aerial fight with the Vulture at the Chrysler Building in the first Spider-Man (2002) video game.
The little boy who loses his balloon in a recurring goal in this game reappears in the Ultimate Spider-Man (2005) video game. He is the first person that the player devours when they use Venom. The part with Venom is a nod to this video game, where the task of returning the balloon back to the boy was considered extremely annoying by game players who played "Spider-Man 2".
Included in the geography is "Ground Zero" where the Twin Towers of the World Trade Center used to be, wait for night and two columns of light can be seen where they were.
During the mission wherein the player is tasked with hunting down Mysterio in his Funhouse of Doom, the clown-like enemies encounters will emit a high-pitched laugh. However, if the player activates their "Spider-Sense" when they laugh, the voice will sound almost identical to that of the Green Goblin from the first game.
Occasionally, a thug might shout out "Time for a little bit of the old ultra violence!" while you are fighting. This is a reference to A Clockwork Orange (1971).