These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
Resulting in in-Universe Nightmare Fuel for Spidey, the moment he realizes that now he will never know if he would let Morlun go or kill him and will always suspecting, to his terror, that he would do the latter.
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 acceptable way before the Other came and threw loads of questions. Which is one of reasons why many people consider is the point the run started going downhill.
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 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 would end...
GodModeSue\Villain Sue: Morlun comes dangerously close to this, with JMS attempting to build him up as the most dangerous villain Spider-Man has ever faced.
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 its no wonder, 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 separate a 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.
Morlun - you can't hurt him, you can't stop him, he will never get tired, never have to rest, will find you anywhere once he touches you and will do anything to get you. If he's after you, your last days are a never ending run with death at the finish. And what's the worst, he doesn't even think about you like a person, just prey and your death is just a part of natural order.
It's not personal.
Shade - he can go anywhere and if he wants, nothing can touch him, so he can go to your house and do anything that pleases him, and you are completely helpless. Did I mentioned he has to trap people in other dimensions for eternity, to stay material?
Shathra - humanoid spider-wasp that paralyzes and lays eggs in her victims, after driving them mad with anger.
Digger - it's zombie-Hulk made from the bodies of multiple dead gangsters.
Gatekeeper - billions of spiders combined in one giant Hive Mind
second Molten Man - not only is he super strong and indestructible, but also a murderous psychopath.
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. Bonus points if you put Straczynski or yourself in his place and change scream from "OSBORN!" to "QUESADA!".
The guys at Spiderfan came awfully close to doing just that with one of their comics, having Peter scream Straczynski at the top of his lungs.