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.
Badass Decay: Several villains. The Lizard in particular gets this bad past his initial appearance.
Broken Base: The quality of episodes after the first season. Some fans think that the show grew the beard after the first season with its story arcs, Character Development, focus on Peter's personal life, others think that the show declined in quality, citing bad animation, constantly recycled footage, the overuse of the Kingpin, Morbius or Madame Web and more space and vampire stories.
Christopher Daniel Barnes as Spider-Man. Many fans think that he is the definitive voice for Spider-Man, like Kevin Conroy is the definitive voice for Batman. But there are fans who think that Barnes was way too melodramatic as Spidey and his voice didn't fit Spidey at all.
Complete Monster: Herbert Landon. In his first appearance (the X-Men crossover), he had his old friend and colleague Henry McCoy/the Beast kidnapped so he could dunk him in the chemical bath he was planning to use for mutant genocide to see if it worked. His later schemes working for the Kingpin involved turning people into cyborgs against their will and generally being a dick.
Carnage, who was as Axe Crazy as the show would let him be.
First Installment Wins: There are fans who see the first season of the show as the one with the most memorable and well-written episodes, like "The Night Of The Lizard" and "The Alien Costume Saga", and with the best animation in the entire series. The following season are more divisive.
Hilarious in Hindsight: In the first episode Spidey complains about why he has to crawl around sewers and can't land an easier superhero gig with the Avengers. He also complains about not being "a galaxy hopping superhero," which he essentially becomes in the final episodes.
In episode 48 "The Vampire Queen" Whistler wonders why all the girls go after vampires and if it has something to do with the fangs. Maaany years before Twilight.
Then there's pre-vampire Morbius, who looks and sounds kind of like Tommy Wiseau.
Jerkass Woobie: J.Jonah Jameson's distrust and dislike of Spidey make much more sense when we learn that his wife was killed by a masked gunman. Alistair Smythe arguably qualifies for this trope, along with Morbius.
Also, the scene where Kingpin's wife leaves him is surprisingly sad and is the one time the Kingpin shows actual remorse for his actions.
You could make a case for all of the antagonists on the chance that they pull an Enemy Mine with Peter.
Hydro-Man. Everything about Hydro-Man. He's an obsessive Stalker with a Crush, and he has superpowers that allow him to get around/into practically anywhere to find you (if you're Mary-Jane Watson) and make him virtually tireless and exceedingly hard to slow down, or even hurt.
The cab drivers from the episode "Attack of the Octobot. Big time, especially Mousie. It's mostly due to their annoying voices. Tina from episode the same episode and "Make a Wish" qualifies to lesser extent.
Take That, Scrappy!: Spidey's tirade against Madame Web matched what many viewers felt about her.
Spider-Man: I am sick of you... and your riddles. And your lessons! And your SUPREME ARROGANCE! Don't you ever, EVER enter my life again! Do you hear me? DO YOU HEAR ME!?
And she did, until the "Secret Wars" episodes. Which she says she foretold about before leaving.
Villain Decay: Many of the villains within the course of the show suffered this. Most glaring would be:
Dr Octopus, who became a mere flunky for the Kingpin, even giving up on his plans to become The Starscream shortly after the time he got defeated by a child.
Hobgoblin, who was revealed to be nothing more than a petty crook and a wuss in his last appearance.
And Alistair Smythe, who Took a Level in Badass by becoming a mutant and leaving the Kingpin's services only to end up becoming a flunky for Silvermane in an even less important position than he was as the Kingpin's lackey.
What an Idiot: In "Day of the Chameleon," none of the SHIELD agents present noticed that "Nick Fury"'s eye-patch was on the wrong eye.
Though, in their defence, they were more preocupied with getting the nation leader's to safter and have probably worked with Fury long enough to over look his eyepatch. Even Spidey was fooled by the disguise until he paid more attention to "Fury's" face.
The Woobie: True to the comics, the sheer amount of crap poor Spidey gets put through over the course of this show, particularly from the second season onwards, is unbelievable.
Iron Woobie: The Scarlet Spider. He's been through all the same trauma that Spider-Carnage has, but somehow came out okay.
Woobie, Destroyer of Worlds: Spider-Carnage. He's psychologically damaged to the point where he wants to die but won't be satisfied until everyone else goes first.