- Peter Parker's father Richard Parker is drawn to resemble how Peter Parker appears in the mainstream comics.
- In issue 3 when Peter gets his superhero name from the wrestling announcer after winning the title he calls him "The Amazing Spider-Man" and "The Spectacular Spider-Man".
- When Peter Parker looks up the Black Cat's father in the 53rd issue, he comes across a list of known cat burglars that includes the names of several established characters associated with Spider-Man, most of whom either don't exist in the Ultimate continuity or hadn't yet been introduced in the Ultimate Continuity: Abner Jenkins (the Beetle), Carradine (the assumed name of the burglar that shot Uncle Ben), Cletus Kasady (the human host of the Carnage symbiote), Dmitri Smerdyakoff (the Chameleon, whose Ultimate counterpart wouldn't be introduced until around nine years later), Hobie Brown (the Prowler, whose real name in this continuity is Aaron Davis), Rick Lawson (the second Prowler), Thomas Fireheart (the Puma), and Martin Blank (the Gibbon).
- Jameson calls The New York Globe "the Distinguished Competition". That's a name that Marvel used to use for DC Comics.
- The Green Goblin is the first villain who knows Spider-Man's secret identity, like in the mainstream universe.
- The first fight between Spider-Man and the Green Goblin (when Ultimate Marvel was still in its early stages, and it was not clear how long would it last) involves a fight on top of the Brooklyn Bridge, as in the classic The Night Gwen Stacy Died. There is no girlfriend involved, but the Green Goblin himself falls from the bridge and it was unclear, by the story end, if he lived or died. Some time later, there is a more accurate adaptation, involving Mary Jane instead of Gwen Stacy.
- Mary Jane Watson especially when she was drawn by Mark Bagley, often wears purple clothes or a purple top, and it's often used in her default picture and how she appears in Ultimate Spider-Man video game. This look is based on the original printing of her dress in the epilogue of The Night Gwen Stacy Died. Likewise she also wears black tank-tops in some issues in allusion to her first appearance.
- One memorable Running Gag is that whenever Spidey swings by the police station, the cops are taking away some screaming nut in a superhero costume who somehow references the latest Crisis Crossover in the main Marvel universe. So far we've seen "Scarlet Witch" claiming that she wasn't crazy (House of M), "Speedball" yelling "Not like this! Not like this!" (Civil War), and "Echo" asking who can you trust (Secret Invasion).
- A girl dressed as Spider-Woman was seen during a story which marked Ultimate Mysterio's debut.
- After his Opposite-Sex Clone leaves, Peter muses on her organic web shooters before dismissing them as a silly idea. During this time, the main Marvel Universe Spider-Man still had organic web shooters.
- At one point, Sam Raimi is directing a Spider-Man movie starring Tobey Maguire. Why does that sound familiar?
- Ultimate Beetle (who has an entirely different origin from 616's Abner Jenkins) wears an armoured suit that looks a little like the classic Beetle, and a lot more like Jenkins's later identity of M.A.C.H.-V.
- When they were about to kiss, MJ said "Face it, tiger, you just hit the jackpot". That's the line mainstream Mary Jane said when she ceased being The Unseen and was actually introduced in comics.
Mythology Gag / Ultimate Spider-Man