- Ass Pull: With Morlun on the ropes, Spidey is forced to consider whether or not he'll violate his Thou Shalt Not Kill rule. Rather than actually resolve the conflict, Morlun's assistant/slave Dex renders the point moot by simply shooting Morlun dead for Spidey. Justified, as it was done to create in-Universe Nightmare Fuel for Spidey, once he realizes that now he will always be suspecting, to his terror, that he would kill Morlun himself. It lacks this justification when the situation repeats itself with Spider-Wasp.
- The Chris Carter Effect: Nothing was ever really explained regarding the whole Totem thing, and eventually it grew into a Kudzu Plot, thanks to The Other (why did Morlun come back from the dead? What was Miss Arrow? Why did the spider-god resurrect Peter after he was 'killed' by Morlun when it would have violated the natural order?) Sad part is that everything was explained in an acceptable way before the Other came and threw loads of questions. Which is one of the reasons why many people consider it the point the run started going downhill.
- Complete Monster: "Shade", real name Jacob "Jake" Nash, from the June 2002 through August 2002 issues, is a criminal who betrayed his cultist cellmate Richard Cranston to steal his ritual that enables access to the Astral Plane. When the ritual was tampered with, Shade gained the abilities of phase shifting and super strength, and began accessing the physical plane by trapping innocents inside the Astral Plane and feeding off their life energy—most often runaway or homeless children—and then uses his time on the physical realm to commit crimes and hire himself out to gang members. When Spider-Man demands to know why Shade is subjecting hundreds of people to the terrible torment of the Astral Plane prison he has constructed, Shade smirks and proclaims "Just for kicks".
- Fanon Discontinuity: Different groups of fans consider different parts of the run as discontinuity. Many fans would rather just forget anything to do with Sins Past or the Totem issue and don't consider them part of Spidey's official universe, for some only Sins Past didn't happen, for certain parts of the fandom the Other and/or everything after it happens in "Quesadaverse" is not regular continuity, and for loads of people there's no such thing as One More Day.
- Faux Symbolism: According to John Romita Junior, it was him who wanted to do the crying Dr. Doom scene (JMS only wanted to put Doom there, the other villains and crying were JR Jr's idea). He also claims that it was only the symbolic expression of how he feels about 9/11.
- "Funny Aneurysm" Moment: After May finds out Peter's secret and tells him gravely that they need to talk, Peter starts worrying and thinking of all the things that she could need to tell him so direly. His mind flashes between "I have six months to live", "Mary Jane has six months to live", "the planet has six months to live"... and then in a moment of levity, to "Doctor Octopus has six months to live. So, do you want to go out for pizza?" Now, over a decade after the scene in question, consider how Amazing Spider-Man ends with Doctor Octopus having only a short time to live... and deciding to take the world with him. Then revealing this was a distraction for his true plan: pulling a Grand Theft Me on Spider-Man, and that it works. Not so funny now, is it Pete?
- Hilarious in Hindsight: The original intent of "Sins Past" was to have Peter be the father of Gwen's kids, but Marvel vetoed that. In other words, a comic book company objected to a development in which their flagship character would've been labelled a deadbeat dad. Heh, heh, heh...
- Never Live It Down: Some people cannot stand that Spider-Man told Morlun that he is the first villain who ever pissed him off. Hyperbole is to be expected, but considering that there's a certain villain that killed his first love it's no wonder that people are pissed at blatant Villain Shilling. There was also the "never been hit that hard before" moment in the same story. Reaction was similar and Peter David couldn't resist poking fun in a Friendly Neighborhood issue.
- The 9/11 issue garnered some criticism for the villains scene, though much of that was the artist's idea and not JMS'. However, during a separate Newsarama interview, JMS responded to criticism with some rather obnoxious insults, saying such things as "move out of your mom's basement" and "for God's sake, stop breeding." These comments dogged him and during Civil War, JMS did another interview in which he claims he was only referring to one particular person, but others had taken him out of context to say he was referring to all of his critics.
- No Yay: The Norman Osborn and Gwen Stacy affair in Sins Past.
- Seasonal Rot: The JMS run is generally agreed to have started out very good, with some cool new additions to Spidey's Rogues Gallery and the introduction of a solid Myth Arc. But then much of his goodwill ended with storylines like Sins Past, and The Other. The Myth Arc thus became a tangled mess and the book went through a horrible Dork Age that took several years to recover from completely. On top of it all, Civil War came along, and Joe Quesada began ruthlessly meddling in nearly everything with the storyline ending with One More Day, one of all the time worst stories, not only in Spider-Man but comics and any media.
- Signature Scene: From his run:
- The entire issue where Peter and Aunt May discuss his Secret Identity and his past. Known as "The Conversation". It was so well liked that a version of it appeared in Ultimate Spider-Man and Kevin Feige cited it as his inspiration for the end of Spider-Man: Homecoming where May learns about Peter's double life.
- "Doomed Affairs" (Issue #50 of Amazing Spider-Man Vol. 2) is known and liked for its instant classic cover art, and for being the issue where Peter and MJ reconcile at the airport and commit to their marriage, while in-between Peter has to stop some assassins from attacking Doctor Doom and later tells the ruler of Latveria to take his gratitude and stuff it.
- Captain America's "Plant yourself like a tree beside the river of truth and tell the whole world 'No. You move.'" speech is from ASM #537, the tie-in with Civil War. It's so iconic it got adapted into the movie.
- The fight scene at the prison in Back in Black between an unmasked Peter and The Kingpin where Peter gives Fisk the beating of a lifetime is considered the high point of the run.
- Squick: The Reveal from Sins Past. Gwen Stacy slept with Norman Osborn, and has children with him. Needless to say, more than a few fans don't take kindly to that. Even those who ship Peter/MJ disapproved of this change and consider it disrespectful to make Gwen cheat on Peter, least of all with the older man who killed her.
- Tear Jerker: Several.
- In the 9/11 issue, when Spider-Man is trying to take a young boy from Ground Zero. The kid explains that he is waiting for his dad, a firefighter, when he sees his father's dead body begin being moved from the rubble. Cue to the scream of despair.
- Peter's fury when he finds out about Gwen and Norman in Sins Past.
YMMV / JMS' Spider-Man