The part where Cloud was dressed up as a Shinra soldier for Rufus' welcoming parade, and the parade's leader asks what they should finish the sequence with. Because of Cloud's previous parade failure, he asks Cloud to tell them what to do. Cloud stands tall and spins his Shinra-issued gun — with the music of the victory fan-fare, just like he does when one wins a battle. Everybody's like, "WOW!!" and "That's awesome!"
In Junon, the party discusses how to get up to the upper level, and it's mentioned that the only way to do so is scale a tower with a high voltage electricity risk. Their unanimous response? "Cloud should be OK then." "Yeah, good luck, Cloud!" "We're all counting on you, Cloud!" And then they all walk away, leaving Cloud stammering, "W-wait a minute!"
If you talk to any of them immediately afterwards, they'll all completely ignore Cloud and chatter away among themselves.
And when he finally reaches the boat after having to go through all sorts of silliness to keep his disguise as a Shinra soldier up, he can potentially find out from Red XIII that his companions realized there was an easier way in by just riding the dolphin to the dock.
Sit your ass down in that chair anddrink your goddamn TEA!
One of the funniest moments in this game was when Cloud decided to dress up as a girl to seduce Don Corneo; he'll never live it down.
Speaking of the Honeybee Inn, going in the topmost door takes you into the girls' dressing room. You typically just go in here to get Cloud some makeup for his disguise, but if you do so before entering a room, you can heckle the girls inside. The leftmost one keeps trying to ignore him, but eventually starts calling him "Pooch" to herself because he keeps stalking her. Not even introducing himself helps the situation.
Not simply mentioning Cloud should crossdress, but then mocking him and calling him "Miss Cloud" for going along with her plan. Seriously, Aerith's personality during the whole Midgar plot arc is pretty surprising if all the player knows about her is her exaggeratedMysterious Waif, Too Good for This Sinful Earth persona from the spinoffs.
If you dress up Cloud in the worst possible get-up, he's resigned to spending the night with a couple of Don Corneo's goons in a small, messy room. Said goons make sexual advances towards Cloud, which, using the game's low-polygon character models, consists of them slowly lurching towards Cloud like zombies.
Especially when Tifa and Aerith catch Cloud almost kissing the old perv. The dialogue before that is particularly funny:
Don Corneo: Is there someone else? Cloud: Yeah, there's this guy named Barret...
Speaking of Barret, "VERMIN? Y'all Shinra're the VERMIN, killing the planet! And that makes you King VERMIN! So shu'up, jackass!"
And another line from Barret when the group's leaving Midgar for the first time is an optional classic. If the player chooses to take Tifa and Aerith as your party members, he'll give Cloud an annoyed "Figured you'd do something like that."
On the other hand, if the player choose to take Barret and Red XIII rather than the girls, they describe this choice as "Very..." "... interesting" (finishing each other's sentence when doing so), then saying "OK, have fun..." "... Boys!"
Who could forget those classic NPCs in one of the many bars: "It sounds like there's something going on outside, but I'm too drunk to care."
Early in the game where Cloud and the others infiltrate the Shinra HQ, one can choose whether to fight the way through the main entrance, or sneak up the staircase in the back. If the player chooses to take the stairs, Barret constantly complains about the huge trek up the stairs, which causes Tifa to snap:
Tifa: Would you stop acting like a retard and CLIMB?! note (Yes, she does use the R-word in the game. Huh)
Late in the game when Cloud disappears from the party, after Tifa escapes the gas chamber and runs out to the cannon in Junon, Scarlet catches up to her and starts to slap her. The player is then instructed to press O (or [OK], in the PC version) to slap Scarlet back. Having to participate in a bitch slapping contest between two women is just plain hilarious.
In the beginning, one can make Cloud choose whether or not to order a drink from Tifa. The choice to get one is "give me something hard." That's not innuendo at all.
Later, when Tifa asks Cloud how he slept, he can remark on how he slept well because it was next to her. If the player chooses this, her response is an amusing "I don't know what you mean."
Most of Cloud's jokes can be extra effective for those who, say, saw Advent Children and Kingdom Hearts first and were exposed to his Flanderized angsty attitude. An especially funny one, if simple one, comes when Cloud gives Yuffie advice on how to combat motion sickness, where he mentions that back when he was in SOLDIER they had to ride in trucks all the time and that "It sucked." Considering the events that immediately preceded this conversation, you wouldn't expect our hero to be in the mood for such a silly line, which makes it even funnier when it comes out of no where like that.
"All right, everyone. Let's mosey."
Also, most of the stuff that comes from Yuffie's mouth.
[Shinra troops ambush the gang] "I didn't plan this one!"
[Cloud debates what to do with a piece of Huge Materia] "Can I have it?"
[In response to Vincent's lament about Lucrecia] "Yawn, boring story #1."
Heck, right before the final showdown she opts to not get in the fight, but proceeds to freak out and claim that the Materia is "all hers".
Not a Yuffie line, but if you get her to go on the date with Cloud, she awkwardly kisses him, to which he doesn't respond, causing these lines:
Yuffie: Say something! Cloud: ... something. [A slapping sound is heard]
Her exchange with her father Godo at the top of the Pagoda - just after a very emotional conversation about the state of the nation and her father's failure to protect Wutai in the war, he orders Yuffie to come back home alive, then lets everyone else go out... and then starts asking Yuffie if the party will be wanting all their Materia after the last battle. His last words to her are something like, "Come back! With the Materia!" Like daughter, like father, eh?
The fight with Palmer. At the end, a truck steals your kill (sort of... he doesn't actually die).
This isn't what you would consider to be a hard battle or anything. Not like the Materia Keeper or Gi Nattack, where you actually had to, you know, try. Fighting with Palmer is more like a personal challenge to see how long it takes to make the battlefield explode into a mess of butter and shrapnel. Palmer stands on one side of the screen, wiggling his fat body about in a presumed attempt to move, or perhaps communicate. Occasionally, he pulls out a gun and fires it at you. But since he went and ate all the bullets, thinking them to be Pez, the thing is running on a combination of materia and AAA batteries, and instead mimics the effects of Bolt 2, Fire 2 and Ice 2. But, he is susceptible to the effects of Stop, meaning that if you've got Seal Evil or some other equivalent on hand, he won't even be able to get an attack off. If you don't paralyze him, it's no big deal, but be warned that Palmer will periodically lean over and slap his ass in an attempt to be provocative, but ends up disgusting you more than anything. Kick his ass to high hell, unloading everything you've got onto the chubby guy. The only thing that will not affect him is gravity-based attacks, quite possibly because a body as large as his tends to produce a gravitational force far stronger than anything you could ever conjure up. Anyways, once you've hurt Palmer badly enough, the Tiny Bronco begins to move. Palmer will turn tail and hobble his fat ass along, trying to catch the vehicle that he is attempting to steal. At this point, the game rewards your patience by hitting Palmer with a truck. To add insult to said injury, your team steals his armor (the Edincoat) before leaving him to bleed rich and creamily.
Aerith's mistranslated line: "This guy are sick."
Red XIII's scene in Costa del Sol. He's found him calmly playing with some kids and their soccer ball... but if the player feels like being particularly cruel, s/he can kick the ball... right into his face. His response is to jump up and bark at Cloud, and if Cloud talk to him after that, he just growls.
Meanwhile, Hojo is chilling out on the beach surrounded by groupies. And "getting a tan" as he puts it... while still wearing his labcoat.
Hojo asks if Cloud wants to be his guinea pig. Later, if you talk to one his groupies, she comments "I'd be happy to be a guinea pig, if it's for Hojo." Though becomes Harsher in Hindsight (or a verydark kind of Hilarious in Hindsight, in a sense) when you learn Cloud WAS a guinea pig of Hojo's before and it's the cause of all his identity problems. Even worse, you also learn his own partner and wife/mother of his child (Lucrecia), AND unborn child (Sephiroth), were his guinea pigs.
Speaking of Hoji, when Red XIII and Aerith are released from a tank in the Shinra building, Red's first action is to tackle Hojo to the floor and bite him. It's rather cathartic to watch, but Hojo's completely played straight complain about it is funny as fuck.
At the Golden Saucer, one can choose to have someone ride the gondola with Cloud. While most of the characters are amazed by the sights and sounds... if Cid is chosen, he just sleeps through the entire ride.
How about Red XIII in a stolen Shinra uniform (with his tail still sticking out), dancing around like a complete moron as he tries to keep his balance on two feet?
The best part is that he's standing frontways, and it's only when Cloud talks to him and he says "I think I pass for a human being perfectly well" that he immediately turns around and the players first see the tail sticking out.
Near Gongaga, the group come across Reno and Rude of the Turks. Prior to this, they've been intimidating and Badass... but here, while they aren't noticing Cloud and Co.'s presence at first, they're gossiping like teenagers about who has a crush on whom (Rude likes Tifa, not Elena, who likes Tseng, even though Tseng likes Aerith...) It gets funnier when Elena walks up beside Cloud and comments on how stupid they're being and insisting that she and Tseng's relationship isn't like that... only then to realize who it is she's talking to and alerts Reno and Rude to your presence.
Another funny Elena moment is later in Icicle Inn, where she confronts the group about Tseng getting almost killed back in the Temple of the Ancients, and she attempts to punch Cloud. The outcome is funny either way: if he dodges, then she swings, misses, falls, and goes rolling out of Icicle Inn. If she decks him then he falls unconscious... and Elena promptly freaks out and feels guilty about this.
The Turks again. Reno, Rude, and Elena are on vacation in Wutai, and refuse to fight as long as they're off duty. When Shinra troops try to get them to help track down Don Corneo, Reno turns the mission down and snaps, "Go away! Just looking at you is making me sober!"
Reno's and Rude's defeat animations. Reno runs for his life, while in contrast, Rude looks down at his watch, then calmly walks away.
The play you're coerced to star in during the date scene, especially if you don't do what you're told (e.g. kiss the Evil Dragon King).
If you mess up lines in the play... FLYING KICK!!!
When Cloud is under Sephiroth's control and about to attack Aerith, the two other characters with you yell out "Cloud!" Except for Cid, who yells out "Dumbass!"
Barret in a sailor uniform. He's twice as wide and quite a bit taller than any of the other sailors, but they don't seem to notice. His in-game polygon model also looks goofy as hell.
Cloud: You look like a bear wearing a marshmallow.
This counts as a possible mood killer considering what happens, but in the PC version of the game, if the player takes Vincent into the Forgotten City, his model begins spazzing out when Cloud go down to confront the praying Aerith, standing with his leg outstretched and his cloak hanging above him. After Aerith's death by Sephiroth's sword, it just gets worse as he walks towards Cloud with one leg pointing towards the sky, his leg outstretched again when he walks in front of Cloud, making him look like he's kicking Cloud in the crotch. C'mon.
Earlier in the same place, during Sephiroth's breakdown in Cloud's flashback, he says "I'm going to see my mother" and skips out of the room. He then proceeds to slaughter the entire town in about 15 seconds, which, while horrible, is pretty goofy when you think about it.
Giving Red XIII the name "Nanaki", when you first encounter him, which makes it hilarious when the party visits Cosmo Canyon later in the game and is surprised that his real name is Nanaki.
Naming every playable character Sephiroth (the story will make hilariously little sense). Alternatively, in the PC version, modding it so all the playable characters' models are that of Sephiroth.
If Cloud does really, really bad in the parade...
Unseen Shinra Exec: That was terrible! Send that soldier a bomb! Game Message: Acquired Grenade!
An often-bypassed scene (due to most people wanting to get the first Huge Materia, and hence not failing the first Submarine Mission) has Cloud and Co. stealing a separate submarine. The players are given a choice of either killing a dog or just subduing it. Subduing the pooch gives this line from Cloud:
Cloud: "Ok, dog, I'm gonna dognap you."
Before that, Cloud and Co. return to dry land in Junon via riding a torpedo. The next scen has Mr. Dolphin (the one who helped the group reach the Airport) bitchslapping Cloud with his tail to wake him up.
Refuse to pay to stow away on the Cargo Ship to Junon.
Sailor: "Thank you. Come back anytime you feel like being stowaways on our ship."
Going on the date at the Gold Saucer with Barret. (Yes, it is possible, there's a FAQ at Gamefaqs dedicated to the date deals.) It's funny but sad at the same time. He enters Cloud's room saying something like "Let's go somewhere that we can talk, in private.") One doesn't get to do the play because the person there sees you two together and says something like "You're our 100th couple... oh wait!" Throughout most of the gondola ride, Barret just talks about Marlene. It's amusing in a sort of weird / dark way how the whole thing is not played for romance at all.
Cid's unexpected flippancy if he's in the party when the Temple of the Ancients shrinks into the Black Materia. Standing on the ledge just before Cloud climbs down to get it, he gets out a cigarette, takes a smoke, and comments on how great it is to have a smoke in a place like that! (Note that this comes immediately before a very disturbing scene involving Cloud and Aeris/th.)
Yuffie's reaction if she's in the party at the Underwater Reactor on the Huge Materia mission when the group encounters Reno and he tells them to "Help load."
Yuffie: "I'm SURE! You want me to do manual labor?"
In a later tutorial level, Cloud explains that since they care about the environment, if the player has too many materia they'll have to trash them... er, that is, give them back to the Planet.
Although it's arguable, you HAVE to admit that the Sapphire WEAPON's last scene is at least a little humorous. After shooting its badass mouth-laser for the first time, it begins to build up energy for a second shot... Only to get its head unceremoniously splattered by the Mako Cannon/Sister Ray. The Mako Cannon/Sister Ray, a somewhat-barely-rotatable cannon that Sapphire WEAPON sits STOCK-STILL IN FRONT OF as its charging up a second mouth-laser, SO stock-still that you don't even see the cannon pivot before firing. There might as well be some comical Failure music playing right after its head gets blown off.