Speaking of which, Squall has several standard move patterns for his Limit Break (with varying numbers of trigger-for-bonus-damage spots) amongst which the game chooses randomly, with some important bosses getting unique ones. The Jumbo Cactuar has this.
Anytime there's dialogue selection in the Laguna flashbacks, there's always an extra option that's shaded in to indicate Squall's reaction to the scene. If you select that, Laguna will react with confusion to "hearing" Squall, which he later associates with hearing "faeries". Made even funnier with the first mind-travel, in which you can select this option repeatedly in a row. Laguna starts talking to himself, baffling everyone around him, until he finally shouts "stop it!".
An early exchange between Seifer and Quistis.
Quistis: Good luck.
Seifer: Instructor... I hate it when people wish me luck. Save those words for a bad student that needs them, eh?
Seifer: [to his lackeys] Add Instructor Trepe to the list.
Blink and you miss it, but just before she says "Good luck, Seifer," Quistis does an incredibly sassy diva head-turn that clearly expresses what she's thinking.
If you chose to walk the long way round the cliff to the Dollet communication tower instead of following Selphie jumping straight down the cliff, there's a brief moment with Zell aping one of Selphie's poses, hopping in place with his arms in the air.
At the end of the Dollet mission, talk to Cid before you get your SeeD results and this happens:
Cid: So, how did it feel out there on the battlefield?
The entire first La Résistance scene and how annoyed Squall is that they're making him fetch Rinoa so they can begin the briefing.
Within that sequence is Selphie suddenly suggesting they blow up the train with a rocket launcher. Which actually might have worked...
How do you discuss things you don't necessarily want your contracted guns (who are in the same room) noticing? Why, crouch on the floor and start whispering, of course!
Then the meeting gets derailed when Zell and Selphie notice just how shoddy the train models look...
Or when you arrive at Timber. The La Résistance member coming to pick you up recognizes that you are the SeeD immediately and asks you for the password. If you get it wrong, however, he decides to lead you to their secret base anyway since "these guys cost us a lot of money!"
When Irvine joins your party for the first time, he arranges party members that would go to Deling City; he chooses Selphie and Rinoa for himself, while Squall gets left with Quistis and Zell. If you chose to agree with his selection, then Selphie and Rinoa would get angry at you then they try flirting with Irvine as payback. All the while Squall has absolutely no idea why the girls snapped at him.
Quistis hanging off Squall's arm only makes it funnier.
In a mild case of Mood Whiplash given the circumstances, Zell provides a bit of funny on one of the train scenes when, in a fit of disgust, he punches the floor...hard enough for everyone, including the conductor to feel it. The conductor even has to come on over the intercom and let everyone know this didn't end up being a case of Nice Job Breaking It, Hero.
When you're going over the plan to kidnap Deling, Zell notices that the model of Deling's carriage looks very shabby and asks if a little kid made it. Zone remarks that the rest they bought from a shop, Rinoa made that one. Rinoa insists she made it like that on purpose, representing her hatred towards Deling. Selphie says "You must really hate him. It's one of the ugliest things I've ever seen".
Later when he's being interrogated by Seifer, he demands Squall tell him "the true mission of SeeD." The player can choose to have Squall lie, in which case Squall bluffs and blurts out that the true mission of SeeD is... to grow flowers all around the world, putting him right into Deadpan Snarker territory. In this troper's opinion, this turns into a Fridge Brilliance moment also, as in the ending, we see Balamb Garden flying over the land... dropping flower petals on the ground below. But maybe I'm reading too much into this.
Considering that the rest of the bogus "true mission" Squall throws out involves waiting for the nations of the world to be lulled into peace by the blooming flowers, and then attacking them... yeah, probably.
Irvine tries to finish off his Big Damn Heroes moment at the D-District Prison by making a casual, sauntering entrance... the effect of which is spoiled when Rinoa kicks him down the stairs and tells him to hurry up and stop trying to act cool.
If you approach the Galbadian missile base on foot when it's time for Selphie's party to infiltrate instead of just driving up in the stolen vehicle, you're treated to a scene of cute, sweet Genki Girl Selphie trying to wheedle the gate guard into letting her and her friends in:
Guard: This isn't some kinda club you can sweet talk your way into. Besides, you're just a kid. I prefer someone more mature.
Selphie: Up yours!
During the battle which erupts at Balamb Garden between supporters of NORG and Headmaster Cid, a staff member and two trained Balamb students corner a SeeD defending two children in the training facility. One of the children declares he will help fight, and one of the students approaches him menacingly...only to reel over after the boy kicks him in the shin.
During the Galbadian Missile Crisis, Squall comes clean to Cid about his resolve to protect Balamb Garden, and Cid says "Quistis was right about you." If you put Quistis in his party, Squall will shoot a look at her as she gets this "I dunno what you're all on about" expression that you will never see again.
Squall, upon discovering the identity of the Garden Master, reflects that come to think of it, he's never heard anything about him before.
The old fisher in FH who's intensely annoyed by your presence but then gets tangled in someone else's net prompting Squall to save him. His reaction is priceless.
For some reason, I thought it was hilarious when Squall said "This guy is sick." about Irvine at the Fisherman's Horizon.
The party's reactions when they go into Zell's room during the events to liberate Balamb in Disc 2.
Bringing Irvine releases his inner child, by firing off the rifles in Zell's Room.
Zell: YOOOOO!! THE HELL YOU DOIN!?!
Squall: (I knew he would.)
And if you bring Rinoa with you instead, when Zell suggests going up to his room she jumps up and down with excitement.
If you bring Quistis, she starts to tell a story about how Zell was riding his T-Board (hovering skateboard) through the hallways and ended up crashing into the girls' restroom, before Zell furiously cuts her off.
If you bring Selphie, she sits on his bed and tells him he should be honoured that a cute girl wants to be on his bed. What's even funnier is that you have the option to make Squall agree with her. If you do then she replies "Squall, you are so getting it."
Zell clinging to Squall's leg after he saved him in Galbadia prison, which ends with him conking Zell over the head for refusing to let go. Then he does it again if you choose him as part of the missile strike team.
When Rinoa makes you take her on a tour of the Garden, if you go into the cafeteria you see Zell throwing a tantrum when he hears they're out of hotdogs (which he'll be hugely embarrassed at when he sees Rinoa there). And if you bring her to the infirmary, Dr Kadowaki will ask if she's Squall's girlfriend. If you reply Yes then...
Rinoa: Whoa, are you serious!?
Squall: I'm serious.
Rinoa: Wow, I'm speechless.
Squall: I'm seriously joking.
During Laguna's flashback sequence at the beginning of the disc, Kiros asks how Julia is doing. During the course of the conversation:
Zell Info Dumping everything that's happened since Squall left for the Esthar moonbase almost borders on Lampshade Hanging. Especially for those in their second playthrough onwards who just skim and tap through the whole thing..
When the party boards the Ragnarok and it suddenly starts moving
Zell: I hope this ain't the case but, I can picture Selphie in the pilot seat, and...
Quistis: ...screaming, 'Whoo-hoo, we're flying!'
Squall: (And standing next to her, a very excited Irvine...)
When asked, Selphie admits that she was poking at the controls and "it just kind of took off."
One flashback to Laguna's time brings up Dr Odine's sorceress research, and his kidnapping of girls For Science!. As the narration continues, we see Ellone crying and Ward about to get rough with Odine, possibly for his attitude, then Odine breaks into an ineffectual escape, followed by Ward in a very anticlimactic low-speed chase in circles inside the laboratory. What really tears it is Ellone getting up and running behind them like it was a game of tag.
If you go to Winhill, taking Rinoa and Quistis, and go to the manor you have the option of starting a funny scene where Quistis scares Rinoa into thinking that the suit of armour is talking to her.