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.
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*
Cait Sith's include "Random Pointless Character", "Annoying Pointless Character", "Harbinger of Misfortune", and "God's Mistake".
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) Cloud:(falling) Aaaaah, I blame you entirely, Tifaaaaaaaaaaaa...
At the Honey Bee Inn, Cloud hallucinates that another Cloud is straddling him as he lies on the bed. He says that he's not that in love with himself, but the hallucinated 'evil twin' tries to get him to give in.
Cloud: Get off me, you handsome devil!
Johnny becomes an Ascended Extra. The author loves to mock 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?
The only time Johnny's Dogged Nice Guy atttitude slips is when he realizes Cait Sith has become one of the main characters:
Johnny:(enraged) Cloud, you f——-, what is that!? You let that thing join your party but not me?!... Cloud:(soothingly) N-no, it's not in my party, I swear!
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...
In the end, as Vincent points out, because of all the backtracking, Yuffie has stolen the party's materia three times in a row.
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.
Cloud:(absolutely resolute) I WILL END THIS!
While trying to save Yuffie and Elena from Don Corneo, the group runs into a Random Encounter with Shinra Troops that were also chasing Corneo. The resulting fight is not only hilariously pointless, but the group's current lack of materia forces them to take down their foes in more creative ways:
Shake reveals her monster form to Yuffie and Cloud:
Shake: THIS IS MY TRUE FORM! (beat) Shake: You are obviously speechless because you have clearly lost this match already. What do you have to say for yourself? Yuffie:YOU'RE A PENGUIN. Cloud: I'm going to have to agree with Yuffie on this one, you are a fucking penguin.
When Yuffie takes down Staniv, he struggles to get up, and declares that she's no match for his War Cry ability. Yuffie then points out that his monster form doesn't have a mouth. One beat panel later, Staniv keels over, defeated.
Yuffie faces the final challenge of the Pagoda: her father.