- In the series premiere, there are a great many gargoyles shown, in reference to director Greg Weisman's series of the same name, also set in New York.
- In the Title Sequence, one of the "photos" of Spider-Man is a tribute to the cover of Amazing Fantasy #15, his debut issue.
- Musical leitmotifs from the 1960s and 1990s series can be heard in the background music.
- In the second season episode, "First Steps," Sandman is stealing the "Urn of Morpheus" from a museum for Hammerhead.
Archmage: Let's not get too overconfident. What exactly have you accomplished? You beat up a beach!
- In the same episode Spider-Man contemplates how to beat Sandman by wondering "How do I beat up a beach?" This would be another Gargoyles reference.
- In the fourth episode of the 1st season, Spider-Man comments to the Shocker/Montana "I mock. I'm a mocker." The Mocker was a comic by Spider-Man creator Steve Ditko.
- The statue of Atlas is a reoccurring feature, likely a shout out to "Atlas Shrugged" in keeping with Spider-Man co-creator Steve Ditko's objectivism.
- In "Opening Night" Black Cat uses a fake ID with the name "Selina Drew" "Drew" is probably a reference to Spider-Woman, aka Jessica Drew, while "Selina" may refer to Catwoman.
- Also in "Opening Night", when Spider-Man is fighting Mysterio, Mysterio sends out some imp creatures to attack him. J. Jonah Jameson, watching from the security room says:
- In "Nature Vs. Nuture" Peter wonders if "Romita's" delivers turkey pizza. A reference to artists John Romita
- There may also be some homage to Batman Beyond Because, at some point during the fight with the Sinister Six (First fight), Spider-Man defeats Shocker the same way Shriek was defeated.
- The battle damage that Spider-Man suffers in his fight with the Green Goblin in season 2 looks like it came from the movie.
- Also, Impact Webbing makes an appearance in season 2. Unfortunately, Venom's are much more effective.
- And then there's this:Spider-Man (To a Mysterio-bot's disembodied head): What are you gonna do? Bite my kneecaps off?
- That one was also used in Weisman's other show Gargoyles episode "Future Tense", where Xanatos said the exact same thing.
- While fighting a giant Sandman, Spider-Man cribs a line from Greg Weisman's time on W.I.T.C.H. regarding the similar villain Sandpit: "How am I supposed to beat up a beach?"
- Colonel Jupiter's Shout-Out to The Six Million Dollar Man.
- Episode "Catalyst" has Peter getting a last dance with Mary Jane.
- "Survival of the Fittest" had Peter cling to a gargoyle that looked remarkably like Hudson to slow his fall.
- Liz Allan's Race Lift to Latina may be a Shout-Out to Paulina from Danny Phantom.
- In "Shear Strength", a demolitions tech refers to "cascading detonations" that would bring a building down "in its own footprint". Which happens to sound a lot like Conspiracy Theories about 9/11.
Shout Out / The Spectacular Spider-Man