Not to mention Hamill's complaint later in the scene about Jay's Pre Ass Kicking One Liner not being in the script. Mainly because it implies everything leading up to that point was in the script.
"THE SIGN! ON THE BACK OF THE CAR! SAID CRITTERS! OF HOLLYWOOD! YOU DUMB FUCK!!"
Also a Crowning Deleted Scene of Funny: "Jay's Dream Date."
Jay and Silent Bob running through the Hollywood back lot trying to escape some guards. They turn and run down one street and WHAM! Crash and fall over thanks to a background piece painted exactly like the real street behind it.
Gordon: Echo Base, I've got a 10-07: two unauthorized on the lot, requesting backup. Echo Base: [over Gordon's walkie talkie] I thought that was a 10-82. Gordon: No sir, a 10-82 is disappearing a dead hooker from Ben Affleck's trailer. Echo Base: [slightly amused] Oh, that Affleck! Backup on the way...
Crowning Blooper Of Funny - when Matt Damon and Ben Affleck are pretending to film Good Will Hunting 2, they repeat a certain 'take' several times because they are corpsing, culminating in them laughing too hard to speak at all. Ben Affleck's high-pitched laugh has to be heard to be believed.
The ending montage, when Jay and Silent Bob use the money they get from the movie rights to hunt down and beat up every Internet troll that bashed the movie.
Having to wait for the businessman on the phone to finish his call, only to just give up and start kicking his ass.
The entire scene with Brent (Seann William Scott) and the girls in the van ("Hey! Watch your language, little boy!"), where Brent is ousted by Jay for being a "dirty sheepfucker!" and thrown out of the van.
In the commentary, Smith notes that a better husband would have given Jennifer Schwalbach Smith more to do (as she completely misses the girls' big scene).