During the first fight between Peter and Harry, when Harry is chasing Peter, an incoming Razor Bat gets stuck to his [Harry's] chest, which he later yanks off.
Goblin Harry getting clotheslined early on, due to the cartoonish “twang” sound he makes when he hits Peter’s web.
J. Jonah Jameson has high blood pressure and medication to take, while Betty Brant has a charge from his wife to make sure he doesn't lose his temper, a long history of being treated like his dogsbody and an intercom with a loud buzzer. Revenge is had.
The buzzer is so loud that when the desk gets rattled every time, it's hard to tell if it was because of the vibrations or Jameson's startled jumps.
Not helping things is that Jameson is having to sit through a terrible presentation about how to try to make the Bugle more hip and attractive to younger readers, which is being delivered by an underling who clearly doesn't have the first clue how to be more hip and attractive to anyone. This doesn't improve his blood pressure.
The little boy who is repulsed by Spider-Man and Gwen kissing.
While probably unintentional, MJ's line to Peter accusing him of a possible relationship between him and Gwen Stacy. "How come you never mentioned her? She's your lab partner, you saved her life, she thinks you're a genius and she had her polished fingernails all over you?" Just the way she finishes with the "polished fingernails" bit makes it sound like Arson, Murder, and Jaywalking, as if Gwen having polished fingernails is part of what's wrong. Then again, MJ issort of the tomboy to Gwen's girly girl in the comics.
Right before that during the exchange with Gwen, Gwen innocently turns to MJ as she says, "it's not every day you get to be kissed by Spider-Man!" MJ, in response, gives a great The Un-Smile and replies, "Can't imagine."
The maître d' at the restaurant repeatedly misinterprets Peter's hand gestures as a sign to bring out the champagne and ring, then has to shoo the other waiters away when Peter corrects him.
Thanks to his heavy accent, the maître d' pronounces Peter's surname as "Pecker".
And the scene where they look? The now legendary moment where Peter comes out of the clothing store with his new look and starts pelvic-thrusting in front of the door. It has to be fully seen to be believed.
Dr. Connors watching the sample of symbiote biomass bumping Peter's blood cells to the beat of the background music.
The moment Peter hears it's Dr. Connors on the other end, he pretends he has been bored to sleep by his mere voice. The rest of the scene he spends by completely ignoring whatever Connors is saying in favor of the cookies Ursula made him. When Connors asks him if Peter has kept the Symbiote with him, he’s too busy talking to Ursula. When Connors is confused by Peter’s non-response, Peter just adds a nonchalant “No, of course not!” without even listening to what he said.
Peter saying, "You're lookin' fine, babe" to Gwen as he walks with her into a jazz club.
And then there's the dance scene in said jazz club, where he starts off playing piano (out of nowhere, really) and then says, "Double time!", jumps over the piano, and walks across the bar (stealing a guy's drink in the process) before doing a ridiculous and impossible slide across the room on a chair. After taking off his jacket (the force of which blows back Gwen's hair... somehow) and throwing it at the stage, he does a stupid little to-and-from slide before saying, in a completely serious voice, "Now dig on this..." before air-thrusting and snapping his fingers to the tune of the music. It's so ridiculously stupid, it's funny.
In the novelization, the keyboardist returns to the stage as Peter gets into a brawl and responds by playing the William Tell overture.
During the final battle, Peter and Harry are flying downward on his glider trying to catch a falling Mary Jane. Peter asks if it can go faster, to which Harry responds with "Hang on!". Peter aptly notes "To what!?"
Also when Harry says "Hey Pete! Am I interrupting!?" when intruding on a Peter/MJ moment.
While watching the final battle, JJJ gets conned by a kid. See it here.
Even better, a background extra stares at the camera when Harry pulls a Vehicle Vanish shortly afterwards, making you wonder if Harry's just awkwardly hiding under the table to dick with Peter.
Most of Eddie Brock's moments before he starts to have his Sanity Slippage.
Eddie: Woah, buddy, love the new outfit. [Spider-Man turns around] It’s exactly what I need to scoop Parker. Gimme uh, gimme some of that web action! [gets his camera ready] Spider-Man:[shoots a web at Eddie’s camera and swings it towards the wall, breaking it] See ya, chump. Eddie: WHAT THE HELL?!
Really Eddie, what did you expect would happen after telling Spider-Man he looked fat?
After getting his Sandman powers, Flint casually tilts his head and lets some excess sand out of his ear. No more earwax with his condition.
This exchange between Eddie and Captain Stacy. Bear in mind they're having this conversation while Gwen is dangling off the edge of a building, about to fall.
Eddie: I don’t know. I just saw her last night. She said she had a modeling gig. Captain Stacy: Who are you? Eddie: It's Brock, sir. Edward Brock Jr. [shakes Captain Stacy's hand] I work at the Daily Bugle... And I'm dating your daughter.
Before Gwen's life was endangered, she was doing some modelling. The photographer was directing her to look sexy and alluring, but the project they were working on was an ad for photocopiers.
The novelization adds some dark levity to the scene above when the phone Gwen grabs while she's falling ends up calling a radio station.
Gwen: Hello! Hello?! DJ:[cheerfully oblivious] You've got the rockin' sound of WKRQ! If you can name our last two "Two for Tuesday" songs, you could be our grand-prize winner! Gwen: Help! I can't hold on! DJ:Right you are! 'Help' and 'I Can't Hold On'! Pack your bags, 'cause you're going on a trip!" [telephone cord snaps, cutting the call]
Finding out that Eddie fabricated the photograph the Bugle ran of Spider-Man as a criminal, Jameson fires him on the spot and is upset that he's having to write a retraction for the first time in twenty years. The retraction is inherently funny if you read Jameson's quote:
"There is no evidence that Spider-Man was involved in the bank robbery, and the Bugle apologizes for any implication of his wrongdoing in the matter," Jameson said, "To airbrush Spider-Man into a photograph and make it look like he's a criminal-that's just something we would never do here at the Bugle."
Also there's the fact that after Peter's famous "You want forgiveness? Get religion." line, Eddie does go to a church... to pray for Peter's death.
Jameson walks in on Peter trying to flirt with Betty Brant on his desk.
Betty:[standing very close to Peter] These shots are so good. Peter:[standing very close to Betty as well] I'd love to shoot you sometime. Betty:[flustered] P-Peter Parker! Peter... [they lean in] Jameson: PARKER! Miss Brant, that's not the position I hired you for!
Right after that, Jonah tries to buy Peter's latest shots. Peter refuses unless he gets the staff job at twice the salary. Then he sits in Jonah's chair, put his feet up on the desk, and eats his candy. Jonah just looks back and forth from Peter's feet to his face with an expression of utter confusion while Robbie seems unsure as to what exactly is happening and Betty laughs in the background.
When Spider-Man confronts Sandman in the armored truck, he initially thinks he's just dealing with a standard criminal, tossing out a classic Spider-Man style quip in the form of "Maybe you haven't heard but I'm the sheriff around these parts." He realizes differently when he takes a swing and his fist gets stuck in Sandman's chest.
After his first fight with Sandman, Peter cleans some of the sand out of his costume and asks, "Where do all these guys come from?"
This little exchange where both Peter and Eddie demand the same camera job from Jameson.
Jameson:You [Eddie] want a staff job, and you [Peter] want a staff job. Doesn't anybody care about what I want? Hoffman:I do! Jameson:[casually, without even looking] Shut up. Get out.
At one point Harry kicks Peter, sending him flying into some furniture, breaking them and quips, “How’d you like that Spidey?” Peter jumps back to his feet and just asks, “That all you got?”, and proceeds to kick Harry the exact same way, except Peter is much stronger, doing double the damage. For added bonus, Peter hurls him through a window in the process, much as Harry had done to him earlier in the film.
Peter:Stings, doesn't it? Harry:[wiping blood from his face] I protected you in high school but now I’m gonna kick your little ass! Peter:[mockingly]Ooh!
In the end, Peter chases Harry to the lab, where Harry accidentally hits a laptop connected to his Sky Stick and it goes out of control. Then, Peter simply dodges one of Harry’s attacks, grabs Harry and pushes him into the out of control Sky Stick’s way, letting it hit him across his face, sending him flying into a bunch of glass shelves, defeating him. Talk about invokingHoist by His Own Petard!
In the novelization, Mary Jane's reaction to her being kidnapped in the climax again is probably the greatest example of Lampshade Hanging in the trilogy.
"Why do they always come after me?" she wondered aloud. "What, do I have the word BAIT stamped on my forehead? Did somebody stick a CAPTURE ME sign on my back?"
The video game
When Venom blackmails Sandman, there's this exchange. Venom's delivery is especially priceless.
There's also something amusing about the symbiote laughing along with Eddie.
Immediately afterwards, Sandman slowly crouches down in defeat as Venom approaches him... and then the drama disappears immediately because Venom does a sassy-ass twirl as he walks.
The scene where Peter flirts with a waitress in the nightclub, Maguire lampshades how one can never tell if the women are repulsed or turned on by Emo Peter, or a little bit of both. Raimi says it is a little bit of both... just like real life!
The comic book prequel
Flint Marko trying to rob a jewelry store only to find it full of cops who showed up to arrest two other robbers.
like someone out of Saturday Night Fever with a spectacularly daft emo haircut and upraised collar, convinced that he's the hot stuff despite the looks of confusion, bemusement and disgust from almost every woman he crosses paths with. The Editor's Cut adds some Black Comedy by placing this scene immediately after Peter blows up Harry with his own grenade.