In the original game, Wedge is set on fire by the explosive charge Jesse uses to get through the door of the first reactor. In this version, Barrett tells Wedge to shut up when he starts freaking out and Wedge just stands there burning.
Jesse gives Cloud a special ID with a picture of her nude on it. It immediately sets off the alarm.
Jesse and Biggs stealing people's clothing and changing in fifteen seconds while the ALARM goes off on the train.
Cloud: "Why did those naked men look like they had been violated?" Biggs: "Are you going to jump or not?!" Cloud: "You stole a man's mustache!"
The recurring gag where people are named after the actions they are doing if their name hasn't been given yet. Like when Aeris/Aerith tries to sell Cloud a flower she goes through half dozen names including "Hemp Pusher" or when they first meet President Shinra he has this speech bubble:
Sarcastic Clapping: *sarcastic clapping*
Tifa's special technique while fighting the giant robot at the second mako reactor.
Tifa: "... Ah, I guess it's up to me now. Time for my special technique." *Starts flailing arms and charges* "NO ONE'S GOING HOME UNTIL I COLLECT ALL THE TABS!" Barret: "Tifa, no, that's too powerful!" *robot explodes and the bridge collapses* Shortly later Cloud: *holding onto the edge* "Aaah, Tifa, what the hell?!" Later Cloud: *falling* "Aaaaah, I blame you entirely, TIFAAAAAAAaaaaaaaaaaaaaa..."
During accidentally hiring a whore, Cloud hallucinates that the voice in his head is the one on top of him and it looks just like him. He says that he's not that in love with himself, but the voice tries to get him to give in.
Cloud: "Get off me, you handsome devil!"
Johnny. Just Johnny. The author loves him and puts him in situations he wasn't in in the game. Every time he appears, it's hilarious.
Johnny: *sees Cloud dressed as a woman* "C-Childhood friend?" "Cloudia": "Not now Johnny." Johnny: *Blushing* "Y-You wanna go out for coffee later, or something?"
After Yuffie steals everyone's materia, Cloud cautions everyone to be careful about random encounters, only to immediately get a game over. He immediately proclaims his hatred for Yuffie, only for Red XIII to ask what he's talking about, because they're back at the Cosmo Canyon part of the adventure... from about eight hours ago.
Cloud: Is THIS where we last saved?!
The best part is Yuffie's indignant expression after Cloud exclaims that she has to die (after all, she hasn't technically done anything YET).
Eventually, they get back to where they were before the game over, when...
Cloud wonders why Cait Sith hasn't died in a while and is told that since he is on his ninth life, Cait Sith might die for real if he dies again. Learning this, Cloud immediately tries to drown Cait Sith.