Connors: Amazing. The tests would show Neogenics was involved! But how could that be? Spidey: That was the category I chose.
After The Beyonder unleashes a horde of villains on an unsuspecting world for an experiment. Spidey mixing incredulity with sarcasm is just hilarious.
Spider-Man: You had to wreck an entire civilization to prove thatevil is bad?
In the Scorpion's first appearance, Spidey's explaining in detail why all the nuclear stuff the Scorpion's messing with is very bad. Jameson asks how he could possibly know all this, leading to this beautiful exchange:
After being surrounded by a few dozen well-armed guards responding to an alarm:
Spider-Man: Hello boys! So, maybe wondering why I called this meeting.
Peter introducing Morbius to Felicia along these lines, especially funny as foreshadowing:
Peter: Felicia, This is Michael Morbius. Michael, Felicia Hardy. Felicia: Nice to meet you. Morbius: The pleasure is all mine. *bows, kisses hand* Peter: Now we really need to go. Felicia: Such a nice man. What movie is he from? Peter: "The Return of Dracula's Ego".
Peter tells Jameson that Spider-Man is going to Russia. Asking why Spider-Man would do that, Peter brings up Jameson's accusation that Spider-Man is a menace to the world. Jameson then theorizes that Spider-Man is going to appeal to the Russians to make him their leader and become a global power.
...and everyone else
In season two, Silvermane accidentally turns himself into a baby trying to recapture his youth. This disturbing scene is turned hilarious two seasons later, when he's regained the ability to speak and picks up running his criminal empire right where he left off, even imperiously ordering his daughter to change his diapers. And then his new attempt to become an adult results in him becoming just as old as he was before due to Vulture being a Spanner in the Works.
Elisa: I'm sorry things turned out this way, father. But at least you won't have to worry about diapers or... Silvermane: I wouldn't be so sure!
Every time baby!Silvermane ever opens his mouth. Just hearing a little kid's voice saying things like "Bah! My mind is trapped!" is hilarious.
Tombstone observing the fight between Spider-Man and Smythe's Mega-Slayer:
Tombstone: Only problem here is, I don't know who to root for.
Tombstone's Narm Charm declaration of "I DON'T BREATHE!" as a cliffhanger while trying to suffocate Spider-Man will have you in stitches.
An alternate reality's Gwen Stacy explaining that she recognized Spider-Carnage as the impostor because he's "as nutty as a fruitcake".
The Kingpin helping save Peter's wedding by completely owning Scorpion with the Mega-Slayer:
Kingpin: Gargan, your corrosives have no effect on this robot! Scorpion: Oh yeah? How about this?! (Scorpion swings his tail, but the Mega-Slayer grabs it) Kingpin: YOU FIGURE IT OUT! (the Mega-Slayer swings Scorpion around until his tail snaps, sending him flying) Kingpin: I broke him? A pity. I was just starting to have fun!
Before that, he and Jameson threw themselves into a contest of one-upmanship regarding helping with the wedding:
Jameson: I know the best pastry chef in Queens!
Kingpin: And I know the Queen's best pastry chef.
A loopy Harry Osbourne singing, "Spider-Man and the Punisher, sitting in a tree! MJ, MJ, MJ and me!"
J. Jonah Jameson: "All the networks are laughing at me. Even FOX!"
When Shocker is thrown into a water tower while his suit is punctured, he's forced to discard the suit before it explodes, leaving him in just his mask and Goofy Print Underwear.