When Spider-Man is hitting the Green Goblin,he says,"Why won't you fall down?". That is a reference to the comics when Spider-Man is fighting Ox and says,"Why won't you fall down?"
At night, if you go to the Sanctum Sanctorum the back door will be open with purple fog spilling out.
Early in development, plans were to have a Hulk and Spider-Man team up. However, the developers opted for Venom instead, because they felt he was more closely related to Spider-Man anyway.
The little boy who loses his balloon is the first person that is devoured when using Venom. This is a nod to the Spider-Man 2 (2004) video game, where the task of returning the balloon back to the boy was a recurring goal in that game and was considered extremely annoying by game players who played Spider-Man 2.
Due to the success of the game, writer of the game and comic of the same name, Brian Michael Bendis, made the game canon to the Ultimate Spider-Man comics, and artist Mark Bagley even added panels that were identical to the game.