Whether intentional or not, Spider-Man makes a reference to Sam Raimi's Spider-Man films during the Black Cat chase. When Spider-Man encounters the armored mercenaries on gliders, he remarks that "Green Goblin is so six years ago! The kids are into Venom and Sandman now!". At the time of this game's release, it had been six years since the release of Spider-Man (2002) with the main villain of the film being the Green Goblin. Venom and Sandman are the main villains in Spider-Man 3 (2007), which premiered a year before this game's release.
If Spider-Man goes to the top of the Baxter Building, there are spider-tokens disposed forming a "4". This is a reference to the Fantastic Four who's reside in and use the Baxter Building as their headquarters.
This game originally was supposed to be "Marvel Zombie: The Video Game" according to a blog post, but was changed because of story problems. This is further backed, as in-game when defending the Stark Tower, at the moment the symbiotes enters the safe area, a message will appear saying, "Remove the zombies from the gate.". This error still appears in the Spanish version of the game.
Many billboards with advertisements that appear throughout the game such as signing up for S.H.I.E.L.D, H.Y.D.R.A. and A.I.M.
If the player uses Spider-Man to smash a newspaper display, the newspaper that will spread in the air are numerous covers for the Daily Bugle used in the Sam Raimi Spider-Man movies, such as "Who is Spider-Man?", "Times Scare", "Wanted", and Spidey and Ock rob bank".