At night, if you go to the Sanctum Sanctorum the back door will be open with purple fog spilling out.
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?"
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.
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.
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.