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Also, JJJ's use of the classic defense, "I have black friends", is actually true, considering his best friend Joe Robertson IS indeed black. This makes it even funnier (along with his lawyer's Face Palm).
Lady Stilt-Man. Even Spidey can't stop laughing... And the way she is defeated is even more hilarious. Even before Deadpool shows up, this is one of the most hilarious issues of Spider-Man in years.
In Avenging Spider-Man, Spidey and the Avengers are a bit of a ways away from NYC taking care of a giant robot attack, and Peter then finds out that none of his teammates are planning on going back to New York at the moment, leaving him in need of a ride. Then a game of "not it" happens to see who gets saddled with taking him home—and that who turns out to be none other than Red Hulk.
Spidey: Someday I'll learn how to fly the jet.
Wolverine: We've heard that one before.
2003's "The Rules of the Game" arc is packed with them. A robot falling in love with Reed Richards, Rocket Racer smacking into a window in an attempt to make a cool entrance, Peter putting on a disguise and getting beaten up at a Bad-Guy Bar... but the best had to be Scorpion being tricked into into breaking his own leg. "If that was... then whose leg is... Oh."
One issue of Spider-Man was called "Slyde Into Destiny". It features Spidey's unknown archfoe, an incredibly minor and deluded villain calling himself "Slyde".
Slyde: That's right, citizens of New Slyde City! You have all been Slyde'd! Slode? Slydomized?
During Mike Wieringo's Spider-Man run, just after he super-evolved and just before the Civil War. Aunt May completely owns, humiliates and scares the living bejeebers out of Tony Stark, Reed Richards and Hank Pym. These three have faced down cosmic horrors from beyond time and space and one little old lady turns them into quivering messes.
Aunt May has frightened J. Jonah Jameson so badly that JJJ has forbidden Peter from ever letting her phone him again. This is a (perfectly normal) man whose reaction to costumed killers tearing his office apart to murder him is one of irritation at how much this is going to cost, and one little old lady had him holding the phone two feet from his ear and cringing. Do not mess with Aunt May.
Sure, the story wasn't great, and they got rid of this as fast as they possibly could, but Peter unmasking on live television, leading to Jameson falling out his chair in shock, was hilarious.
Spider-Man: A-ha! I knew we had something in common besides our love of tights! You're into old movies too, huh?
Batman: I was - when I was young.
Spider-Man: Young? Somehow, I can't picture you ever being young! You must've been pretty cute, waddling around in your diapers, chasing the Joker across the playground!
Batman: I was never "cute".
In one occasion the FF had to Spot the Imposter between Spider-Man and the Chameleon. Ben solved it by throwing both of them down of the building, with poor Chameleon being recognized when he started screaming while Spidey just spun a web and flung himself away.
The two-parter "Hyde and Seek" is full of humorous moments, such as Spidey suspecting that danger's "right around the corner", only to find that Hyde has thrown an entire corner of a building at him. Or Spider-Man showing off a defeated villain to someone saying "Daddy, Daddy! Can I keep him?"
Amazing Spider-Man #699, as Peter Parker, trapped in Dr. Octopus' body, attempts to figure out how Ock was able to swap bodies with him, starts to look through Ock's memories... and finds out he and Aunt May did the nasty!
Peter:[Mentally] NO! NOOOOO! [Vocally, as Doc Ock] ...Ahhhhhh!
Amazing Spider-man #600, as J. Jonah Jameson was officiating his father's marriage to May Parker and had just asked if anyone had any objections.
Anyone? This's your window. Right here. Take your time, I can wait.
*sigh* Very well.
Whenever Peter’s Spider-Sense goes into overdrive, it becomes ridiculously thorough…
Truck: Huge machine of metal and death!
Stapler: Pending impalement!
Elevator: Might stall!
Random Slob: Ate burritos for lunch!
Peter: "Shut up spider sense! I can cling to walls; I’m not going to fall down the stairs!"
All of "The Commuter Cometh" from Amazing #267. Poor Pete just goes through one sort of hilarious mishap after another, from being chased by a guard dog to getting kicked off riding off the top of a bus for not having any fare on him.
While not a comic, the novel New Avengers: Breakout by Alisa Kwitney has a fantastic moment where Spider-Man gains entry to the Raft while the other members of the team are hunting down Electro. Going off a hunch, Spider-Man walks down a hallway in the raft filled with imprisoned villains (including Doc Ock and Carnage) and bribes information out of them by offering them doughnuts. Doc Ock even begins tearing up when he hear's they're from a coffee shop whose cinnamon rolls he adores.