On the level entitled "Building Top Chase", there is a billboard to the side at the start. If you climb onto it and crawl around to the front, it will show an ad for Tony Hawk's Pro Skater 2 (2000) and Spider-Man will say: "Tony Hawk. Hey, I skated with that guy!" (Spider-Man was a secret character in Pro Skater 2.)
In the "Building Top Chase" level, one of the nearby cranes can be entered. Inside is the lair of the Green Goblin, one of Spider-Man's deadliest enemies. Though he does not actually appear in the game, it's nevertheless something of a thrill for the hardened fan.
In homage to the classic Marvel series "What If?", this game has a "What If?" mode that can be accessed by the password screen, introduced by the Watcher (as the original comics were). With this mode on, you can play through the game and observe the (frequently hilarious) changes that have taken place. Changes range from insignificant alterations to complete deviations from the original premise.
During "What If?" mode other Marvel characters can be seen in the background, including the Watcher (introduces "What If?" mode), the Silver Surfer (when Spider-Man is pursued by police and take a ride on the blimp), the Ghost Rider (very briefly seen driving down the side of a building at the very beginning of the "Race to the Bugle" level) and the Sub-Mariner (seen outside during the battle undersea with Carnage). The Sub-Mariner even gets an entry in the game's character database.
In some versions of the game (not the Dreamcast version), entering "RULUR" as a cheat code will cause J. Jonah Jameson to be replaced by Neversoft's own J. James Jewett throughout the game (who also gets an entry in the game's character database).
When wearing the Spider-Man Unlimited costume (the one that gives the power of invisibility), Spider-Man can turn invisible during the bank levels and walk up to the robbers, listening to them exchanging small pieces of dialog with each other.
If a swear word is entered in the cheats menu, Spider-Man will pop up from the bottom of the screen and give it a smack. Additionally any swear words entered as the file name are automatically changed to other words (e.g. "sugar").
On the Item Hunt training course, if you collect every token above ground, then descend underground and go through the door marked "?" all within one minute, you enter the Kraven room, based on Kraven the Hunter, one of Spider-Man's oldest enemies in the comics.