Plenty of these pop up if you examine things in the puzzle sections thoroughly enough.
Separated by puzzle:
- 3rd Class Cabin (prologue/first puzzle)
- Repeatedly examining the ladder by the bunk bed with the blue suitcase.
Junpei: (So, ladder, we meet again.)
Junpei: (Once again, I gaze upon this stately ladder.) "Ladder? I don't even know her!"
Junpei: (Most. Original. Joke. Ever.)
Junpei: (As I gaze into the ladder, the ladder gazes into me.) "Hey, so did you hear what that shopkeeper said after his ladder got stolen?" "No, what'd he say?" "Further steps will be taken."
Junpei: (...And that's why I have no friends.)
Junpei: (The ladder watches me. I sense that it finds me...wanting.) "So this friend of mine fell all the way down a 15-foot ladder." "Wow, that's pretty bad. How's he doing?" "Oh, he's all right, but he's feeling pretty rung out by the whole experience."
Junpei: (I should be writing these down... They're comedy gold!)
Junpei: (I think the ladder is following me.) "Trying to keep up with all the latest stiles has me all rung out..." "Well, if it's a choice between being a step for someone else, and being a real social climber, I'll take the ladder!"
Junpei: "What do you call a secondary ladder covered in people?" "A full B-ladder!" (Okay, I need to stop doing these before I hurt myself... Beside (sic), this is no time to be making jokes! I need to get out of here, now!)
- If you play the game's demo where Akane wakes up in the same room as Junpei, there's a scene when she climbs up the ladder to the top bunk bed that leads to this Suspiciously Specific Denial:
Junpei: I-I'm not using the reflection of the water to look at your underpants!
- 2nd Class Cabin (Door 4)
(examining the painting in door 4)
Lotus: What about you, Junpei? Does it look anything to you?
Junpei: Hmm... I guess it looks like...
Junpei: Hmm... a funyarinpa? See...? I mean this totally looks like one... Here, and here...
Lotus: What the hell is a funyarinpa?
Junpei: What do you mean "what the hell is a funyarinpa"? You mean...you don't know?!
Lotus: How the hell would I know!?
Junpei: How could you not know?! That's...that's practically blasphemous. Say you're sorry! Apologize to the funyarinpa! Goodness, you are such a rude woman.
Lotus: Junpei, are you just screwing around?
Lotus: Forget it.
- In room 92, examining a light, of all things.
June: It's light.
Junpei: Even if it's heavy?
June: That's light!
- Checking the lit candle when in the same room as June.
June: Jumpy, you lit the candle.
Junpei: Yeah. You want me to light your heart on fire?
June: Jumpy... Don't quit your day job, okay?
- Lotus's commentary on the mirror.
- If you refuse Santa's gift of the clover bookmark, he will instead give it to Lotus.
Santa: Hey, you old bag! This is just the right gift for a woman in her forties!
- Lotus giving you "hints" when you repeatedly examine the empty curtain rod while having the curtain in your inventory, but not as your active item.
Lotus: There's a curtain rod on the ceiling.
Junpei: Yeah, there is.
Lotus: There's a curtain rod on the ceiling!
Junpei: Wh-Why does that make you angry?
Lotus: The ceiling! There's a curtain rod on it!
Junpei: Okay, okay, I get it.
- Kitchen (Door 4)
- Examining the pots and pans.
- Junpei's "chunk of meat."
- Looking at the sharpened knife in the freezer.
- Examining the bottle of oil in the kitchen area.
- If you're playing the section via Memories of the Escape (which glosses over some things, usually long or important scenes, with the explanation that Junpei 'can't remember what happened here') and don't pick up the pork before leaving the freezer, Junpei has this response instead of Santa taking it:
Junpei: ... Whoa... I have... no idea... what's going on... What am I... Why am I holding a frozen hunk of pork...?
- There are several meme references in this room too, for some reason. "Well, excuuuuse me, Princess!" and "Why so serious?"
- Upon looking at some pots and pans repeatedly:
Junpei: Hey, did you see that action movie that came out last week?
Santa: Nah, I heard it was critically panned.
: Actually, it's pretty good if you have some pot
- Operating Room (Door 7)
Junpei: The organ is...
Junpei: Really, Clover? I expected more from you.
Clover: Oh, like you could have done better!
Seven: Hey, Junpei! There's dihydrogen monoxide on this shelf!
Junpei: Why don't you just say "water"...?
- Checking a bottle of purple liquid around few times.
- The innuendo of playing with the medical mannequins and using them for... other purposes.
- Chart Room (Door 1)
- Examining the compass leads to this exchange:
Junpei: A compass...
Ace: And what destiny does it point us to...?
Junpei: I really hope you don't think that sounded cool.
- Examining the broken engine order telegraph:
Ace: Ah, a human hammer. They're often used to subdue large men like Seven.
Junpei: Ace... You really kinda suck at making jokes...
Ace: ...That was rather cruel...
- Captain's Quarters (Door 1)
: Look, a hook. *Beat
* That's not a joke!
Ace: If I sit in it, will you let me be chairman?
- Also, if you look at some of the equipments laid on the table, Junpei'll remark that it looks like a monkey with glasses and a steam engine model.
Junpei: Actually, it looks more like a guy who've watched too much TV...
- Library (Door 9)
- More puns and innuendo from checking the books.
: It says "Riemann Hypothesis
". What is there to hypothesize about with a reamin'? Isn't it pretty straightforward?
- There's a book titled "Mindswap" on one of the bookshelves. It's about switching bodies, and Clover remarked that she's fine switching bodies with Snake or Junpei, but not Seven. She then calls Seven out for thinking about it.
- A rather random moment between Clover and Junpei:
Junpei: (So many books here... I wonder what this one's—whoa! What's this? ...Warm...?)
Clover: *blushing* Oh...! S-sorry!
Junpei: Oh, uh, no... I'm, uh, I'm sorry...
- Study (Door 9)
- The pipe cheer. Has to be seen to fully enjoy it, as the animations make it twice as funny (especially Snake's reaction).
Seven: Gimme a "P"!
Clover: Gimme an "I"!
Snake: Give me a "P" and an "E"!
Junpei: What's that spell?! Pipe! What the hell are we doing...
- Examining the monitors on the ceiling has Junpei ask Clover to hang from them.
- Checking the compass after finishing the puzzle leads to Junpei making a few puns about directions. And if you examine it one more time after that:
Junpei: I wonder what sort of dye reaction Zero needed to get Snake's robe to look like that... It's really quite fetching.
- Clover congratulates Junpei for yet another job well done:
Clover: Yay! You did it, Junpei! Good boy! Who's a good boy!
Junpei: Agh! Knock it off!
- 1st Class Cabin (Door 5)
- Examining the vase when in the bedroom.
Snake: A vase? Where did you find this?
Junpei: Over in the kitchen.
Snake: I see... Well, I suppose that might be useful for bludgeoning Seven over the head.
Junpei: That's not what we're using it for.
(after filling it with water)
Snake: So, you've filled the vase with water, have you? I assume you intend to dump it onto Seven's head? Hmm... Not a bad idea. Very well. I would appreciate it if you would put this plan into action post-haste.
- Checking the light switch in the hallway several times leads to Seven composing a short song for Junpei (then adding a verse). Junpei is not amused.
Seven: Hey Junpei, you're a Taurus...right?
Junpei: ...What? Why?
Seven: Well, you're so well-organized. Most people wouldn't bother to search something that didn't seem to mean much.
(After examining the light switch a few more times)
Seven: Hey, Junpei, I wrote a little song for you. Take a listen. "The Ballad of the Well-Organized Man"...
Seven: ♪ Well-organized... Well-organized... ♪ You're orderly, but not an orderly... ♪ ...That ain't no bull.
Junpei: ... (Urge to kill...rising...)
(After examining the light switch again)
Seven: Hey Junpei, I wrote you another verse... Listen...
Seven: ♪ Well-organized... Well-organized... ♪ You've got it all laid out, when you're not out getting laid... ♪ Not a torus but a Taurus.
Junpei: ... (His death will be slow.)
- Examining the shower head in the bathroom:
Seven: Testing, testing. Hey, it's great to see you all here. I just flew in from New York, and boy are my arms tired! Yes, thank you, I'll be here all week! Try the veal!
Junpei: That's not a mic, Seven. It's...just a shower head.
Seven: Wha—?! What the hell?!
- Examining the toilet paper in the toilet.
: Two toilet roles here, one for business, one for fun.
- Examining the toilet paper a few more times in the toilet
Junpei: All right, I'm gonna pull off some of this toilet paper! Rolling, rolling, rolling... Rolling, rolling, rolling...
Seven: Hey Junpei... I don't really think you need that much...
Junpei: ... Well, let's just wipe the slate clean then, shall we?
- Examining the bed a few times whilst facing the piano.
Snake: Junpei, I cannot help but notice your interest in the bed. Perhaps you are hoping we will spend time on it, together...
- Examining the chair to the dresser whilst facing the door to the hallway.
Junpei: (It's a small, round chair. Looks like it probably goes to the vanity)
Snake: Oh... Wow, this fabric feels great. I bet that chair's really comfortable.
(after examining it a few more times)
Junpei: (Squish... Squish... Squish... Squish...)
Snake: Junpei, how long do you intend to abuse that chair? I suggest you finish soon. Otherwise, I may be forced to teach you a lesson in physical pain.
Junpei: (His face might look calm, but there's a monster under there. Gotta admit, I'm a little scared...)
(examine it again)
Junpei: (I don't wanna get my ass kicked by a blind guy, so I think I'm gonna leave the chair alone. ... For now)
- Seven's commentary on the mirror.
- Examining the mirror
Junpei: (…And there we are in the mirror. A college kid and a terrifying giant of a man in a beanie. Stuck in a cramped bathroom… With this beast of a man… What would my parents say?)
- Casino (Door 5)
- Examining one of the chairs whilst facing the fireplace in the casino.
Junpei: (This chair goes to the poker table. Hmm... It feels really soft...)
(after examining it a few more times)
Junpei: (Squeeze... Squeeze... Squeeze... Squeeze...)
Snake: Are you quite finished with the chair, Junpei? If you don't stop this behaviour at once, I will be forced to teach you a lesson you will not soon forget.
Junpei: (His face is as calm as ever, but his voice... Terrifying...)
Junpei: (I don't wanna get beat up, so maybe I'll just leave the chair alone for now.)
- Checking the chandeliers a few times from behind the bar.
Snake: Junpei, why do you talk to yourself so frequently?
- Examining the bottle of drink on the counter leads to some amusing dialogue with Seven. Attempting to go back to the rest of the room multiple times after unlocking the door leads to some more.
Seven: Junpei! If you really want this, you're gonna hafta get through ME first! You can't even guess at my true strength! If you don't wanna die here, turn around!
Snake: Would you, ah, like me to leave you two alone together?
- Only switching on the right-hand light over the fireplace then examining the canvas leads to Junpei misinterpreting the symbols on it.
- Laboratory (Door 8)
- The 'Science Boy' thread of dialogue in the laboratory (gotten by examining the mannequin multiple times after getting the activation key).
Junpei: The mannequin looks sad, I'm starting to feel bad for it.
Junpei: Am I getting attached to this thing? Maybe I should give it a name... How about the Science Boy...?
Junpei: Science Boy is lying on the table. His poor head is full of electrodes.
- Gets pretty ridiculous after Clover accidentally sets the mannequin on fire. Examining the mannequin will have Junpei worry about Science Boy more than Clover, much to Clover/Lotus' annoyance.
Junpei: Science Boy! Noooooooo! Oh, the humanity!
- If you click on the laboratory door several times once it's unlocked.
Junpei: (So long, mannequin... You may not have been a real man, but I always thought of you as kin...)
- Steam Engine Room (Door 6)
- The flight of stairs that's perfect for looking up skirts. What makes it hilarious is that Santa asks for Clover, not June. Actually Fridge Brilliance: June is Santa's sister.
Santa: Oh man, Junpei, I can't believe I missed something so important!
Junpei: What's so important?
Santa: Look at those stairs... Look at them carefully! That gap! That height! That angle! It's perfect!
Junpei: Perfect? Perfect for what...?
Santa: Whatever, just bring Clover here, right now! Tell her she needs to walk up and down these stairs!
Junpei: Huh? (Clover's not here... what the hell is he talking about?)
- Santa calling the cloth bags in the corner a 'snowman secret meeting'.
Santa: Look, Ace! It's some kind of snowman secret meeting!
: Those are just bags full of sand. You use them as a counterweight when you're lifting something with a pully system.
Santa: Man, you're too serious...
- Examining the catwalk multiple times leads to this:
Junpei: It's the catwalk, meow.
Santa: You want me to push you off her, Junpei?
Junpei: No way, meow.
Santa: You jackass...
- Examining a barrel under some stairs:
: We should get Seven to throw the barrel from the top of the stairs. It'd be just like that old game
- Cargo Room (Door 6)
- You'll get an amusing reaction for examining half of the cards. For example, Junpei (and Santa) will act like a narcissist to his own card, June will be embarrassed at her own card, while being jealous towards Clover's card.
Junpei: There's a pretty cool-looking dude on this card. I can't take my eyes off it.
Junpei: There's a pretty cool-looking dude on this card. I feel...enraptured...
: There's a pretty cool-looking dude on this card. I just wanna rub my face on it.
Santa: Man, the guy on this card is one good-looking son-of-a-bitch! Way more class than that other chump...
Junpei: Hey! What's that supposed to mean?!
Santa: Huh? What's your problem? Didn't say I meant you, did I?
Junpei: There's a picture of Lotus on this card.
Santa: Man, her hair is ridiculous. It's like...clay, or something...
Junpei: Says the pot to the kettle...
- Shower Room (Door 3)
- Confinement Room (Door 2)
- Examining a certain part of the ceiling repeatedly.
Junpei: It's a ceiling. I've seen a lot of ceilings in my time. I'd say this one rates about a 3, 3.5.
Junpei: So that's the ceiling, huh... I wonder if it's sealing us in?
- Lotus refusing to touch the toilet, ever.
- Junpei's fixation on pulling the third room's toilet string
- Torture Room (Door 2)
- The semi-running gag about pipes.