Anticlimax Boss: Kraven the Hunter. He's built up as a highly skilled warrior who decided to take down Spider-Man. Peter isn't even remotely interested in fighting him (he'd just beaten Doctor Octopus at the time) but when Kraven insists, Peter simply dodges a few times then knocks him out with a single blow. Instantly lampshaded by Spider-Man.
Peter: Huh. I thought he had super powers or something. Showbiz phony.
Arc Fatigue: Many felt that the Double Trouble Doc Ock/Kraven the Hunter arc ran too long.
Spider-Men, the crossover between the 616 & Ultimate universes to celebrate the fiftieth anniversary of Spider-Man's first appearance — is it a great idea, or yet another case of Quesada dropping the ball, given his previous comments on the matter of a 616/Ultimate universe crossover. Is it too soon to have Miles meet 616!Peter since the former is still finding his feet as a superhero, or just a wasted idea since it comes the year after Ultimate Peter was killed and shortly before 616!Peter is as well? The latter in particular, as it completely dropped the plotline going through the end of "Men".
Creator's Pet: Kitty Pryde became Peter Parker's girlfriend in and, after they broke up, remained a part of the cast and was fit into as many plotlines as possible. Brian Michael Bendis has gone on the record to state that he's always liked Kitty Pryde from back when he was a kid and that he enjoys using her... combine that with a statement he made about Peter "being him" and the conclusion to come to is pretty easy. Some don't mind the attention paid to her... but others do.
Gwen Stacy. So much so they eventually brought her back.
Jessica Drew is easily one of these, having minimal screen-time but a huge fanbase.
Miles' supporting cast is getting popular, such as Ganke and Rio Morales.
Foe Yay: During the "Return of the Green Goblin" arc, we get to look at things through Norman's eyes during a conversation with Spider-Man. The voices in his head tell him things like "kill him" "skin him" "burn him" and "kiss him".
Back in the early nineties, one of the most famous songs by Italian band 883note that now, by the way, is no more since its lead singer is now pursuing a solo career was titled "Hanno Ucciso L'Uomo Ragno", which is Italian for "They Killed Spider-Man". Fast-forward by twenty-years-or-so.
In "Cats and Queens", the focus of MJ's story was her wanting to run away from home so she and peter could be married, with him saying he'll always be there for her. Also in the same arc, Black Cat tells him he'll have seven years bad luck. This was in 2004...
Similarly, every time the subject of sex came up between Peter and MJ, they resolve to "wait until they're older".
At July 2005's San Diego Comic Con, in response to the question the Ultimate & 616 universes crossing over, Joe Quesada stated that he'd rather close down one universe than have them cross over because it meant they were officially out of ideas. Fast forward to 2012, and Marvel announced that they will be having 616!Peter crossing over to the Ultimate universe to meet Miles.
Ho Yay: Apparently Miles and Ganke gave this off to Miles' parents...not that they mind. Doubles as Mistaken for Gay.
Jefferson [after talking with Miles about his relationship with Kate Bishop ]: Good to hear. For a while there I thought you and the Gankster had a thing going. Miles: What?! Jefferson: Frankly, your mother thought that years before— Miles: Mom thought that Ganke and I were...together? Jefferson: Nothing wrong with— Miles: Ew.
A small detail, but in the 2004 "Hollywood" arc, when Peter fights Doc Ock on the set of a new Spider-Man movie, a black stuntman in a Spidey outfit hits Doc Ock with a camera. When he tells Spidey that he's just a stuntman, not the actor playing him, Peter says "I thought I got revamped there for a second..."
In one of the first issues, a photo can be seen that shows a young Peter with his aunt and uncle at Disney World. This was many years before Disney actually purchased the company.
Magnificent Bastard: Kingpin, he makes Lex Luthor look like a chump. For example - he bought out the wrestling company that Spider-Man made his first few public appearances for prior to becoming a superhero, purely so that he could make money over Spider-Man's likeness & knowing that Spidey's choices were A) quit being Spider-Man, allowing his profile to fall & kill off the demand for Spidey merchandise so Fisk couldn't profit from him, but at the cost of being unable to stop his operations; B) publicly unmask to claim ownership of the Spider-Man likeness & stop Fisk from merchandising it, but making his loved ones targets for Kingpin; or C) let him get away with it. Fisk even points out that if Peter quits, he'll just hire a new Spider-Man to make sure that people still want to pay for Spidey merch.
The final issue of Fallout ends with Nick Fury confessing to MJ how he feels responsible for Peter's death. In the middle of it, he admits he had been "grooming" Peter to be a super-hero. Not the best choice of words, given the unpleasant other connotations that word has in the twenty-first century.
In the middle of his long rant at Miles and Spider-Woman, Roxxon randomly yells "childcare" for no readily apparent reason.
In issue 13 of the relaunch, both the original Peter and Jameson are tied up after being caught by the Chameleon siblings. While the brother was robbing a bank as Spider-Man, the sister took on the face of J. Jonah Jameson (but with a scantily clad female body) proceeded to shoot the original Jameson in the head. Right in front of Peter. Ugh.
The storyline in which Deadpool and the mercenaries take Spider-man and the X-Men to face "justice" on that game show. Starts with a school full of unsuspecting people getting knocked out and kidnapped and ends with them having to rescue Xavier, who is stripped, chained up, and has his eyes pried open ala A Clockwork Orange, so he is forced to watch his students be killed.
Venom's portrayal in this series is absolutely nightmarish. The suit, rather than simply making you more aggressive like in the mainstream verse, seemingly drives its wearer to near insanity even giving them delusions to make them attack people (Peter ditches it after it makes him see a random burglar as Uncle Ben's killer before driving him into a murderous rage). Also it apparently feeds off its hosts like a parasite, driving them to try and consume people to stabilize itself. And it gets even worse after getting attached to Conrad Marcus; he becomes a hulking Implacable Man monster that Miles can barely hurt and unlike Eddie Brock, he goes hunting after Spidey's family and friends, ending with him tearing through a hospital trying to kill Rio. And he succeeds.
Though in the latter two cases, they actually did come back.
Unnecessary Makeover: Mary Jane was on the receiving end of one via Liz Allen in one story, which involves wearing incredibly skimpy clothing and dying her hair black.Said arc wasn't very popular. MJ herself even hates it, and quickly ditches it the first chance she gets.
Carol Danvers qualifies over and over again. She refused to just put Norman down, instead, every single time she chose to keep him alive in a prison he's proven capable of breaking out of at will. This reaches critical mass at the start of The Death of Spider-Man - not just Norman, but five other dangerous superpowered criminals break out of the Triskelion, all of whom are enemies of Spider-Man, and the last time five of the six teamed up, it required the Ultimates to stop them. So she not only sends the Ultimates off to fight Nick Fury's Avengers to cover her own ass, but she doesn't even tell Spider-Man that six of his enemies have all escaped from incarceration, all so that she can keep the breakout a secret. And the kicker? Because she inadvertently caused the death of Spider-Man, this wound up being the straw that broke the camel's back and got her fired from her position as Director of S.H.I.E.L.D.
Eddie Brock Junior gets major points here. After being told by Peter that their fathers' life's work is actually dangerous in the extreme, and that Peter, a guy with superpowers, barely survived using it for a few hours at most, Eddie decides the best thing to do is get the other sample he had hidden, and stick his fingers in it. And as a result he ends up stuck in a living nightmare, hunted by a megacorp with an unrelenting hunger driving him to eat people.
Narm: Spidey's game over screen is pretty melodramatic, with the web-slinger exaggeratedly falling to his knees as the ashamed faces of his loved ones look on in the background. It becomes even more hilarious if you failed something as simple as catching up to the Rhino after you exposed his weakspot, making it seem as though Peter had absolutely failed everyone by not being able to stay close enough despite the villain only traveling to a parking lot not far from where they started.
Nightmare Fuel: Eddie hunts Trask down to his "golfcourse prison" ready to get revenge. When Trask stammers about the guards, Eddie becomes Venom and says in a terrifying tone "They are not nearly well armed enough." His victim doesn't last long.
Then again, Venom in general qualifies, as the Ultimate incarnation is by far the most unsettling portrayal of him.
Take That, Scrappy!: The first person that Venom kills in the game is an obnoxious little kid with a balloon, in a nod to the Scrappy Mechanic balloon missions from the Spider-Man 2 game.