During Yosuke's story mode, he discovers everyone's acting weird because it's an illusion to get them to fight each other. Yukiko said that Yosuke kept demanding her to wash his back, which leads to this:
Yosuke: Wha-well, never mind that. Yukiko, have you seen a girl around?
Yukiko: No, I'm sorry, but I haven't...did you want her to wash your back?
In Yu's story mode, Teddie asks him to bring back a nurse porno because Yosuke's mom destroyed his stash. And whenever Yu brings it up, Yosuke flips out.
Yosuke: WHAT'S WRONG WITH NURSES?!
Also, this line when Teddie brings up the nurses in front of the whole Investigation Team in Yosuke's story mode.
Yosuke: (When did this conversation go from working to wanking in just two steps?!)
Aigis in her Story Mode after defeating Naoto… during their conversation, Aigis thinks of Naoto as a she (Mitsuru and Akihiko both still think Naoto is male), and Naoto comments on Aigis not hiding her true appearance, leading to the following exchange:
Aigis: I am curious, though. When you refer to your "true appearance," do you mean the fact that you are a woman?
Naoto: [surprise] Wh… what?
Aigis: Am I mistaken?
Naoto: [evasive] Oh, um, well…
Aigis: Your clothing hides it, but my sensor scan shows the body measurements of a human with female proportions.
Naoto: [shocked, blushing] Wh-what do you mean!? How much can you see!?
General Teddie: [interrupts on monitor] Hey, hey, enough with the chitchat! Hurry up and move on to the next—
Aigis: [ignores him] Would you like to know your current measurements? From top to bottom, they are…
Naoto: [interrupts, blushing again] Th-that's quite all right!
General Teddie's eyes widen and he pants pervertedly.
General Teddie: Never mind little old me! Please, finish that line of thought. I demand it!
Naoto: How did we get so off subject!? If you're going to go, please hurry and leave!
The whole exchange between Yu and Yosuke in the latter's story mode. Due to the effects of the illusion Yu seems pretty… protective of Nanako.
Yu: How dare you, calling her "Nanako-chan" in that intimate way!?
Yosuke: Yes, sir! I'm sorry, sir! Umm, forgetting Nanako… san… for the moment, it seems like there's someone here besides us. She can't use a Persona, so I thought maybe she was dropped in here… Uh, Yu?
Yu: Why would you forget Nanako!?
Yosuke: That's ridiculous! I mean, c'mon, Nanako-cha… san really likes you no matter what! She's always telling me how you're such a nice big brother and how you're so cool!
Yu: Yosuke... enough. You "always" talk to Nanako? Why? Where? What do you mean by "always"? What was the precise date and time when you spoke to her!?
Yosuke: Oh crap, I was lying, I'm sorry!
Yu: What…? You were lying!? Are you saying Nanako doesn't like me!? That she doesn't think I'm nice or cool at all!?
And later on in the conversation, this:
Yosuke: (To himself) Ahem… sorry, Nanako-chan. (To Yu.) Haa haa! That Nanako-chan! What a dummy, right!?
Yu: That's it… your life is forfeit!
And then, after their fight, Yosuke briefly forgets that Yu was speaking under an illusion and calls him "big bro" to cheer him up. Yu says that he isn't comfortable with Yosuke calling him that.
The fight between Chie and Yosuke in, once again, the latter's story mode counts as this.
Not to mention Yosuke outright admits he mistook it for something more…intimate at first.
All this after saying this when they first meet:
Chie: Oh, it's Yosuke… what a letdown.
Early on Yosuke comments about having Teddie keep the TVs up in the TV world in case someone gets trapped there and Chie mentions that no one would be careless enough to fall into the TV. Kanji falls into his family's new TV after falling asleep. Not to mention half of Kanji's story which includes his joke path that he's still thinks he's in dreamland seeing his wish came true all the sudden without realizing.
In her story mode, Naoto meets up with Akihiko, who proceeds to lecture her on taking care of her body while flexing.
Akihiko thinking Teddie is called "Teddie Teddie" because of how Teddie introduced himself, and still referring to him as "Teddie Teddie" in his narration after Teddie corrected him.
Kanji's route is a goldmine of laughter.
Kanji: Now get back inside me!
Teddie: I-I don't swing that way!
Mitsuru's story, beginning, when she first met Akihiko eye-to-eye:
Mitsuru: Akihiko, what on Earth are you wearing?
Akihiko: Hm? Didn't I tell you I was on a training expedition?
Mitsuru: Don't tell me you came here from the airport like that… Does the concept of keeping a low profile mean anything to you?
Aigis: Mitsuru-san, I believe we have lost the right to complain about that.
Mitsuru's narration: …That's it. I'm never mentioning the subject of our appearance again!
Everybody has something to say about what Akihiko is wearing:
Naoto: He's the perfect example of someone who should be detained for questioning.
Numerous comments have also been made about the conspicuous eight-door limousine they ride.
Aigis: (riding limo) Mitsuru-san. Our activities are supposed to be undercover, correct?
Aigis: For undercover missions, it will be necessary to keep all personnel and vehicles from being noticed.
Aigis: Mitsuru-san. May I say something that I've been meaning to say for a while now?
One of Yukiko's motives for fighting: revenge for her boxed lunch! Gets turned Up to Eleven in her joke ending. How much? First she force feeds her boxed lunch to Yu (after fighting him), who subsequently passes out (and she thinks he's sleeping comfortably as a result), then later offers the same to the rest of the Investigation team, all of whom balk, but eat it out of respect, making her think they're happy to eat it. Last of all, she attributes everyone getting sick later on to different causes other than food poisoning.
Akihiko badgers a bartender for protein. The bartender thinks protein is a code word and Akihiko is going through some sort of withdrawal.
The only moment when a true man can cry according to Akihiko.
Akihiko: A true man is only allowed to cry when he loses his wallet!
Chie: Y-Yes, Master!
In the beginning of Aigis' story, as Mitsuru tells her to investigate the hijacked plane for "sensitive" cargo…
Aigis: Mitsuru-san's cargo… sensitive belongings for a vacation… Ahh, I understand. Hijacking a plane out of a desperate desire for undergarments… this incident will surely go down in history.
Mitsuru's eyes bulge at the unexpected comment.
Mitsuru: Wha-!? You're jumping to conclusions! It's not "sensitive" in that way!
In Yu's story, after the battle vs Aigis, ELIZABETH just bursts right the hell out of nowhere and asks for Yu to fight. Yu's total confusion at the fact that she even wants to since there's no point in it, and Elizabeth's constant mispronouncing of words end up probably making it one of the best parts in Yu's story.
Elizabeth: This encounter has borne much flute.
Elizabeth: Flue? Chimneys? Something to that effect.
To say nothing of Yu's inner-monologue noting his relief that he didn't meet Elizabeth instead of Margaret when he was a regular guest of the Velvet Room.
During Yosuke's story, after beating Yu, Yosuke remembers that Kanji's nickname was Beefcake Emperor and starts to panic rather spectacularly about the condition of his hind quarters. When he finds out that Kanji was already beaten by Teddie, Yosuke expresses his relief about how his "ass is safe".
Aigis' narration of what happened after the Investigation Team and Shadow Operatives returned to the real world through the Junes television.
That was practically the biggest goldmine of laughs after all is said and done. When they finally got out of the TV world, practically all the customers took pictures of the group especially since they consist of a woman in a spy catsuit with a fur coat, a half-naked guy wearing a cape, a pop star idol, a famous boy(girl) detective, two robot girls (One of which carrying a Axe the size of a desk), the local store mascot, and the rest of the investigation team.
And of course, Cops ensue, and everything proceeds to run like hell out of there, Labrys, being a Fish out of Water, has no idea what's going on, Teddie, being stupid, also does not. Rise is more concerned with her Phone, Kanji is trying to pick a fight every once in a while and Naoto repeatedly stops him. This is all conveyed in text but nevertheless, it's hilarious.
Labrys' annoyed grunt and flailing legs when she stuck half-way through the TV because the axe/thruster combination that attaches to her back is too large.
Aside from the general hilarity of watching Kanji smash through the tournament all while thinking it's a dream, there's also the fact that a lot of plot-critical elements (such as the involvement of the Mysterious Entity in the tournament's events) simply fly right over his head without him noticing them.
In Yosuke's story mode, Yosuke makes a heartfelt speech about his friends to Aigis... and then butchers the last word by mistake. Which Aigis repeats.
At Yukiko's joke ending, when she comes across Yu, there's no illusion confusing their words for either of them, but Yu attacks Yukiko after she offers her boxed lunch, thinking the real Yukiko would never endanger her friends like that.
In Naoto's story mode, after she and Mitsuru fight, they discuss the fact that illusions were warping each of their perceptions of what the other was saying:
Mitsuru: In that case, I'll… well, I'm willing to forget all the things you said about my body.
Naoto's narration: Wait, what? Her BODY!?
The final boss in Teddie's story mode. It's just Kanji, who thinks the tournament is still going and wants a fight. And Teddie goes along with it so he might be able to get Labrys to kiss him.
Yosuke's inner-monologue describing Chie, Naoto & Rise as the "We're-Actually-Sensible Team" during the ending of his story mode.
When Chie sees real Teddie for the first time in her story mode, he makes a funny noise.
One of Chie's Victory Pose sees her entering a crane stance and Tomoe materializing in front of her, blocking her from the audience's view. Chie then proceeds to walk around her Persona and pose for the camera again.