JMS Spider-Man/YMMV

"It's not personal."
 * 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.
 * 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.
 * 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 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.
 * Complete Monster: Morlun, to the point Spider-Man was so close to breaking the Thou Shalt Not Kill with him that the only other time he was this serious about taking a life was after the Green Goblin killed Gwen.
 * 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.
 * God Mode Sue\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.
 * High Octane Nightmare Fuel: Many of the new villains.
 * 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 hell of 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.


 * 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 pretty much 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.
 * Never Live It Down: Some people cannot stand that Spider-Man told Morlun that he is the first villain who ever pissed him off. Because Peter never was prone to hyperbole.
 * Ruined FOREVER: Complaints about the totemic subplot are often made.
 * 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. 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.
 * Woobie, Destroyer of Worlds: Two. New Digger has a little bit of it, being shocked by how much the world changed when he was dead. Charlie Whinerman is second.