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There are a few gems during the first dining hall meeting.
After Maizono discovers the fridge and Yamada expresses concern about food supplies:
Fukawa: Y-you can just eat sesame s-seeds or something...
Yamada: Huh? What am I, a parakeet?
After Fujisaki expresses concern about Monokuma appearing before Maizono in the kitchen:
Asahina: But was everything okay? He didn't try to like, eat you or anything?
Yamada: E-Eat her...? Um, what do you mean by that? I mean, when you say "eat," what kind of eating are we talking about?
Asahina: C-Come on, man!
Kuwata: What the hell, fatty!? You're acting like some kind of sleazy drunk dude.
Hagakure: Not like there's a good kind of drunk dude...
Fukawa resents being with Asahina and Oogami:
Fukawa: S-Stop trying to drag me farther into y-your meat dimension!
Given their preoccupation with protein, one suspects that Asahina and/or Oogami may have been regular patrons of Aiya in better days.
Naegi and Maizono run into Enoshima in the school store:
Enoshima: Damn, Makoto! I never woulda guessed, but you're a total player, huh?
Maizono: No, no, it's nothing like that. I'm his assistant!
Naegi:To be dismissed like that is somehow...
Enoshima: Huh? His assistant? What is that, like some new kinda roleplay thing? Well, whatever. What you're into is your business. I don't judge!
Maizono's cooking specialty? Chili oil.
Naegi's epic pratfall after Monokuma interrupts his moment with Maizono.
I aimed at Monokuma, and punched with all my strength.
And then missed with all my strength.
And then fell down with all my strength. And hit my back with all my strength.
The entire sequence during the investigation involving the trash room. From Kuwata accusing Yamada of volunteering to be janitor because of untoward designs on the girls' trash, to Yamada adding that his 2D exclusivity also includes 3D merchandising, to Togami suggesting they deploy Ogami to keep the boys on garbage duty honest, all the way to Yamada speculating that the inexplicable fire in the incinerator is the work of elves (or fairies).
At one point in the first trial, after someone points out a suspicious lack of hair at a crime scene, suggesting the culprit was someone who had no legitimate reason to be in the room and cleaned up after themselves:
Celes: Maybe you cleaned up to erase traces of Maizono-san visiting your room... ...isnít that also a possibility?
After it's revealed that Oogami and Asahina have alibis because they spent the night together, Ishimaru attempts to reprimand them over the inappropriateness of a man and woman sleeping together. Oogami has to remind him that she, too, is a woman. It gets even weirder in the demo, where the sleepover part is cut out, so Ishimaru takes issue with a man and woman drinking tea in the cafeteria together.
Yamada says any man would've jumped at the chance to go to Maizono's room at night... except him. Because he's only into 2D. In case you forgot.
During the trial, Yamada blurts out the following when Oowada asks about the culprit:
Yamada: I'm sorry, but I give up! Quit without saving!
During the trial, Monokuma answers a theoretical question by saying an accomplice to the culprit wouldn't have a shot at graduation. People start to assume this means there couldn't have been an accomplice since one would have nothing to gain. Fujisaki points out that they didn't know this until now, so there still could've been an accomplice. Monokuma snaps that there is no accomplice! Oops...
Makoto: (thinking) That's what I've been trying to tell you...
Monokuma attempts to motivate the students to commit murder by threatening to reveal their "darkest secrets" to the entire world unless one of them commits a murder. The funny one is Naegi's, simply because it's such a banal "darkest secret" compared to the eventual culprit and victim's secrets: Naegi used to wet the bed until 5th grade.
The segment in the beginning with Monokuma attempting to lead the students in a morning exercise session surely counts. Particularly the fact that Ishimaru was not only going along with this unquestioningly, he was the only one doing it at all.
Yamada and Fukawa's back-and-forth in the library after the second floor opens up.
Ishimaru and Oowada have a willpower contest in the sauna, complete with matching battle auras.
Same chapter (and also the anime, episode 4), there's also Yamada accidentally pressing Celes' Berserk Button by serving her improperly prepared royal milk tea...
Celes: (cute smile) Even in cafes that offer proper milk tea, it is always more expensive than simple tea with milk. It takes more time to prepare, surely, but...why even bother creating a menu if you are not going to offer the highest level of quality!?
Yamada: Well, um...we don't actually have a menu...
Celes: (completely pissed off) That does not matter. Hurry up and bring me what I asked for, swine!
Yamada: WHAAAAAT!? O-Okay! Your little piggy will bring it right out!
Celes: Hmhm. I do so love coercion.
Punctuated by the soundclip used in the official English version: Celes growling "You little BITCH!" without her French accent. Also doubles as Foreshadowing for Chapter 3... In any case, Naegi's inner monologue stating that Celes is "one scary chick" is definitely an understatement.
Genocider Syo (alternately, Genocide Jack/Jill) is a goldmine for these; using Naegi as a punching bag during a Relationship Values moment, and describing Togami's underwear with a Godot quote come to mind.
Her rant about how she can't be the culprit. The very last reason? She doesn't know how to make tight knots.
Her extended analogy comparing murders to Italian food and ramen.
Also, the start of a brief Running Gag: Makoto becomes "Big Mac," and Chihiro becomes "Cherry."
Togami: No, I am not...effing with you right now. I'm telling you the truth.
From the Zetsubou Translation: Ishimaru and Oowada's breakfast scene has them ramp up the obnoxiousness by replacing their "anikis/kyoudais" with bro puns.
Ishimaru: You're wasting your breath, Broseidon... a woman could never understand the depth of two men's bonds...
Oowada: Well said, Broski... mind if I get a tattoo of that somewhere,
Ishimaru: Your parents only gave you one body, Browada. You should really take care of it!
During the trial, Kirigiri is asked to explain why she concluded Oowada was the culprit. The player gets to answer for her, and one of the options is "Because I hate him."
Yamada, Ishimaru, and Hagakure have their own reasons for not inspecting a corpse:
Yamada: Examine her...carefully? Like, using our hands? Nowaynowaynowaynoway!
Ishimaru: It's...probably best if I don't run my hands all over a dead girl's body...
Hagakure: I-It's not that I'm creeped out or anything. It's just...based on religious grounds, ya know?
Even Fujisaki's Unsettling Gender-Reveal has some of this. Kirigiri won't come out and say Fujisaki's a boy, instead telling the others to thoroughly pat down the body, which leads to an unwitting Oogami volunteering for the task and roaring in shock when she finds out. Then the others react.
Yamada: Ah, I see. So "she" was actually a he. Thank you for confirming this fact.
During the Machine Talk Battle against Ishimaru, it's possible for him to say "Show me some evidence!" and "I won't listen!" in rapid succession, as if one moment, he's challenging you to defend your argument, and the other, he won't listen to anything you have to say. It's a bit of a tragically funny look at how in denial he is over Oowada being the culprit.
Genocider Syo makes fun of Asahina's... assets throughout the chapter:
Genocider Syo: Jeez, your knockers are HUGE! What the heck, did you convince them to double up on milk production?
Genocider Syo: What's your top power level, like 35-22-33!? You start out big on top to try and look thinner down south!
Genocider Syo: Look at your melons! They're seriously gargantuan! Do you dunk 'em in milk every night or something!?
Slightly later, when Hagakure tries to reassure Asahina:
Hagakure: As a matter of fact, one time I thought I'd spotted a Grey alien, but it turned out to be a tadpole!
Yamada's initial reaction to Kirigiri's technical description of the AI Fujisaki built. Particularly Hilarious in Hindsight.
Yamada: So you mean... this is a program for the dumb users who canít even bother to open Google and search for things themselves?!
Slightly different in the official English translation, as Yamada is reacting to Naegi's questions about the AI Fujisaki built:
Yamada: If you wanna know more... just Google it, okay!?
Yamada later declares Alter Ego to be "the most EXCELLENT 2D possible."
Hagakure: But he's a guy! And also a computer program!
Yamada: Oh, that aspect is no problem.
Monokuma tries to figure out what everyone was doing in the changing room:
Asahina: Y-Yeah, just because you demand something, doesn't mean we have to do it!
Monokuma: Do it...? You mean, like *do it* do it?
Asahina: Wait, what? What do you mean, *do it* do it?
Monokuma: Ewww, gross! You said "do it"!
Asahina: What!? You said it first!
Celes successfully covers for them by saying the girls won rock-paper-scissors to see who gets to use the bathhouse. Monokuma tries to entice the boys to spy on the girls with talk of a "man's fantasy." Naegi convinces Hagakure and Yamada to back down, but he later admits that he was reluctant to turn down Monokuma's offer. See also the Easter Egg mentioned further down.
Togami and Fukawa's reactions to the group being late to the gym:
Togami: Did you forget how to walk? Is that why you're late? It's simple—right foot, left foot. Right foot...
Fukawa: I hope you all win the l-lottery and get hit by a b-bus...
Right before that, Togami wishes he could go on a shooting spree.
Togami's reaction to Monokuma's bribe.
Naegi: A figure like ten billion yen... that's...
Togami: ... way too little.
The official translation changes it to $10 million, which Togami maintains "is not nearly enough."
"Ishida": I'm gonna stick a banana up your tailpipe!
The scene where the others find out that Yamada's developed a... thing for Alter Ego.
Hagakure: I happened to do a psychic reading for a certain famous CEO once... And that guy was seriously head over heels for a mannequin. He had a wedding and everything! And your eyes just now... I saw the same look in HIS eyes!
Yamada:(shouting) Shut up! Sheís not a mannequin! Sheís an ANGEL!
Yamada:(composed) And don't bother telling me angels exist! What we have can't be defined by your petty "words"!
Followed shortly by:
Yamada: I found myself, y'know...liking her. Her face, her personality, her voice. Even her keyboard...
Ishida and Yamada come to blows over Alter Ego:
"Ishida": Moron! Talk down to me and I'll ram my fist right into all four of your vital points!
Yamada: Well *I* punch at the speed of sound! And I don't have any arm hair, so there's no drag!
Followed by Oogami promptly shutting them both down.
The picture of the 'strange person', and the nonplussed reactions it gets out of everyone.
And later in the trial when they're discussing what the two people in the photo were actually doing, two of your options amount to "They're drunk" and "They're dancing."
The search party discusses warning yells.
Celes: So... is something like "KYAA!" fine?
Asahina: You can shout "KYAA" or "YOOHOO" or anything you want!! Just shout loudly so we can hear you!
Celes: Heh heh heh... "Yoohoo" is amusing. This is the first time I've heard someone suggesting that kind of a warning yell...
And then later she actually shouts "YOOHOO!"
Yamada: Donít put me on the same level as that...that...virgin! I might catch his virginity!
Hagakure: Nah, my guess is you're already infected...
Asahina:(taken aback) Wait, can you really catch it!?
Celes:(smiling) Stop being vulgar. Let's eat breakfast.
Togami's response to one of Syo's romantic propositions:
Genocider Syo: You don't have to play hard to get, Master! You can just play hard!
Togami: That doesn't make any sense...
Byakuya started to slowly back out of the room...
He started picking up speed, and soon he was sprinting out of the dining hall.
Earlier, the revelation that Togami's hiding out with a stack of books in the pool changing room.
Genocider Syo announcing her mission is to redeem the reputation of alternate personalities everywhere who have been stereotyped as cheap plot devices, for justice!
When Kirigiri finds Hagakure stuffed into a locker.
Kirigiri: He was fast asleep when I found him. I had to kick him a little to wake him up.
Hagakure: That was too cruel! You should be more gentle when waking people up, 'right? Like, by pushing their belly or something!
Kirigiri: ...That's just gross.
When Naegi questions how Kirigiri could search a dead man's underpants when her examination of a body turns up some evidence hidden there she replies:
Kirigiri: They're just underpants. It's not like I put my hands inside his socks...
Once it comes up at the trial and others are understandably taken aback, Naegi ends up telling them with an awkward expression that the pants aren't the important part. Then when he has to answer a multiple-choice question about who something was sent to, one of the options is "Hifumi's pants." And then when he gets another question about something two people have in common, one of the options is "The paper hidden in Hifumi's pants."
Naegi: That's right. We found it stuffed in his pants.
Asahina: What!? In his...
Genocider Syo: ...pants!?
Oogami: Hm. Yes. His pants...
Naegi: Okay, well, forget about the pants for now.
For bonus hilarity, in School Mode we get a visual on the underwear in question: it's a Justice Robo thong.
Continuing from the above, Asahina has the following to say when Naegi gives the pants as an answer:
Asahina: His pants...? Are you saying his pants are...alive!?
Asahina: Are pants people!? Are there PANTS PEOPLE!?!?
Celes: I couldn't take it! I hated it from day one! More than anyone anyone ANYONE else in here! I wanted to get out! Every day was fresh torture! And you wanna know why? HUH!? Because...I had a dream.
Hagakure's rant about how his fortunetelling has nothing to do with the occult, which then gets derailed into a discussion of his personal experiences with cattle mutilation, which involves an alien-abducted burger that turns out to be partially made of pork...
Hagakure: Now do you see!? THAT is cattle mutilation!
Naegi: I...kinda got lost halfway through...
Asahina: I can't tell if you're for the occult or against it. You stink of stupidity...
Prior to the ride down to the fourth trial, Monokuma claims to have discovered the power of emoticons, demonstrating how smiley faces make any negative thing sound happy and how sad faces do the exact opposite.
Monokuma: The ultimate martial artist! ^_^
Monokuma: A locked room murder mystery! ;)
Monokuma: You're at a picnic and you find a dead body! XD
Monokuma: Do you have a hundred friends? T_T
Monokuma: Now then, please get on the elevator! o_O
Monokuma: I'll see you all down there! <(*-*<) ^(*-*)^ (>*-*)>
Apparently Monokuma already knew of the power of emoticons beforehand, as he and Hagakure use them in an exchange prior to Monokuma instituting the rule against busting locked doors:
Monokuma: I'm not mad! >_<
Hagakure: You're totally mad! ;_;
Hagakure malaprops his way through the early part of the fourth trial, substituting "dying message" with "shining message" and "vienna sausage." Asahina doesn't even know where to begin with that latter one.
During the fourth trial, when Kirigiri brings up the subject of the Monokuma bottles:
Fukawa: What does ch-chess have to do with anything!?
Hagakure: Yeah! Shogi is way better!
Fukawa: Yeah! ...Wait, n-no! That's not what I mean!
Later during the fourth trial, Fukawa insists that she didn't disturb the crime scene, even though it becomes increasingly obvious that she did, leading to:
Togami: Stop wasting my time. Just tell us the truth.
Asahina and Hagakure talk about the sprinklers in the greenhouse, which gets derailed into a discussion about Hagakure's stupidity:
Asahina: Well, you don't have to worry. They say idiots never catch colds, ya know.
Hagakure: Of course not! Cuz idiots never get wet!
Naegi: Umm...I think you're talking about ducks.
Asahina: I'm starting to worry about you, Hiro. Can you tell me what ten plus ten is?
Hagakure: Hey, come on! You don't ALWAYS have to call me dumb! I may have been held back three times, but that doesn't make me stupid! But if it'll make you happy, I'll answer your dumb question...! So! Um...what was the question again?
Asahina: Don't worry. You just answered it...
Hagakure suggests using the lawnmower in the greenhouse toolshed to call for help by making crop circles.
This exchange during the group's attempt to break into the headmaster's office:
Hagakure: I'm all flubbust—no... I'm totally flabbag—flapstaf—
Genocider Syo: Fapsauce!?
Fukawa's wonderful explanation of the wolf tattoo on Chapter 5's victim:
Fukawa: Her master m-must have made her get it...to be like, "You're my b-bitch."
Hagakure's dogged insistence that Kirigiri is a ghost, forcing Naegi to prove that she's still alive, with Togami washing his hands of the whole debacle and Kirigiri standing right there.
Asahina: But...she has legs and stuff.
Hagakure: Well that's just because...
Hagakure: ...she's like the latest evolution in ghost technology!
Togami: There's a limit to how much ridiculousness I can tolerate...
Naegi's paranoia over the chickens in the greenhouse, coupled with Hagakure's paranoia over plants.
Naegi: They're...just regular chickens, right? Like, they don't eat people, or lay bombs instead of eggs, or something crazy like that...?
Hagakure: Don't you get it!? Don't you realize...the true horror of plant life!? It's just there, just beneath the surface. Beneath their calm exterior, they're always watching, and waiting... And when they decide they can't leave us in charge of Earth anymore...they'll put their plan for global human extinction into action!
When first confronted by Naegi and Kirigiri in the gym after their escape, Monokuma uses a ton of especially lame bear puns in conversation with them.
Fukawa has this to say if you decide to talk to her:
Fukawa: This smell is s-so...smelly...! Ahaha! Super smelly! You smell even w-worse than me! Way worse than me! ...I win.
Hagakure asks Naegi if he went to the spirit world and spoke with Miss Cleo. Naegi expresses bewilderment.
Asahina thinks the door to the Monokuma control room is booby-trapped. She tells Naegi to go in first.
Asahina briefly assumes direct control over Monokuma: "Groooar! Gimme all yer donuts!" Then she finds the self-destruct button on the control panel. Naegi has to convince her not to push it.
When Genocider Syo reverts back to Fukawa prior to the start of the trial (right after declaring intent to kill the mastermind, no less):
Kirigiri: No human language can describe the disappointment I'm feeling right now.
During one of the Non-Stop Debates:
Fukawa: You didn't d-deny me this timesy wimesy! Agh! You made me go all cutesy!
Hagakure: Don't worry. There wasn't anything cute about it.
At one point in the final trial, Monokuma's shouts out two of Creator/Falcom's titles successively as an Oh, Crap reaction, which is Xanadu and Faxanadu. Even better? Those lines are voiced. Unfortunately, it loses some of its impact in the NISA translation, but "Xanadu times two" still has a ring to it...
Monokuma calling Celes "Celestia Lu-whatever" (when he would otherwise refer to the other dead students by their full names) while listing the names of the dead students who could possibly be the mastermind.
While also pretty nightmarish, the reveal that society has turned into a dystopian Monokuma-themed world is incredibly surprising and kind of hilarious. Naegi's simple "What the..." response sums it up best.
Enoshima: *Creepy Monotone* Okay, okay, that's enough of your little lover's quarrel.
The Big Bad, on successfully baiting Togami by mentioning the Togami Corporation:
"You bit into it like a middle-aged secretary at an all-you-can-eat cake buffet."
Hagakure's consternation on realizing that, if the revelations are correct, he's twenty-two (twenty-three in the NISA translation) and still in high school.
One of the pictures that Monokuma gives the characters showing their school life before their memories were erased includes Oogami pulling a Shoryuken on an inflatable shark with Yamada thrown into the air.
Enoshima's face being accidentally covered up by Ishimaru during a group photo is kind of funny, too. Until you find out it's a plot point.
Even better: In two of the other photos, Enoshima's face is hidden because she has her back turned to the camera. In the pool photo, however, it's hidden because she's getting splashed in the face by Kuwata. This goes further in the anime, where in Fukawa's wintertime picture she's being smacked in the face by a snowball.
After the final trial, Fukawa expresses her desire to have a child with Togami. Togami being, well, Togami, he has this to say in response:
Togami: Please, stop. That would be a greater horror than anything I've encountered so far.
Nothing will get in the way of Asahina's preoccupation with donuts. NOTHING. Also pretty heartwarming and awesome, as it's a perfect demonstration of the hope that Naegi and the others had fought so hard for.
Hagakure: And what're you gonna do if there *are* no donut shops? Or donuts?
Hagakure's first scene in his social link has this little gem when he attempts to predict Naegi's future:
Hagakure: It would appear that the mother of your children, and the mother of *my* children, are the same woman!
Naegi: I refuse! Denied! Don't like it!
Since Hagakure says it was a "trial run," the "discount" he tried to give Naegi earlier doesn't apply. Said discount is just $100 off his usual going rate of $1000 for two hours, at least in the official English translation. Then Hagakure offers to do a second reading to check the veracity of the first one. Additional fees apply, of course. Given his self-proclaimed accuracy rate of 20%...
In any case, Naegi's desperate prayers afterwards sell it even further. Also want to know something funnier? Make the wrong choice and this ends up happening at the end of chapter 5.
In Hagakure's third Free Time Event, when he asks Naegi about UMAs, Naegi can reply with "Thurman."
And in his last scene he asks for Naegi's kidney, or failing that his identity.
In Celes' free time events, you can listen to her talk about her gambling exploits, all of which seem to be ripped straight out of various manga. One of them, she describes as the greatest crisis she ever went through... only she suddenly diverges from the story to talk about how she accidentally spilled tea on her dress during the tournament. The rest of her tale is about how she barely managed to get to the dry-cleaners in time to remove the stain.
Naegi: *to himself* You can't just say stuff like that!
There's also Celes' ranking system. Naegi now ranks as a C, which Celes claims is a great honor. Naegi's inner monologue isn't too impressed, though.
During Asahina's last free time event, she asks Naegi to pretend to be her boyfriend so she can have some practice when she finally finds a partner. When Naegi asks what to do, Asahina pauses, and then announces they should "begin":
Asahina: Oh, darling! You're home! Are you ready for dinner? Or should I get a bath going?
Naegi: Wait, Hina... That's more like a stereotypical 1950s married couple than anything...
In one of Kuwata's events, he loudly expresses his dream of becoming a punk rock star, and Naegi thinks that he can't criticize that passion... and then the background music cuts out with a slam as Kuwata reveals it's all because he's trying to get a date. His last event has him claiming he's been "brainwashed by baseball" in an attempt to deny that he actually misses playing.
When Oowada asks whether Naegi prefers cats or dogs, he can Take a Third Option and reply "Bears." Oowada is not amused.
Naegi manages to keep Ishimaru from confiscating his trendy hoodie by claiming the hood doubles as a safety helmet.
Yamada's third Free Time Event involves him going through Diet Coke withdrawal, complete with hallucinations.
Genocider Syo's nicknaming tendencies go Up to Eleven in Free Time Events. Apart from Big Mac in the trials, Makoto gets saddled with the names Mahkyutie, Mackie Chan, Macoco Chanel, and Macarena.
Pretty much anything to do with Syo results in some hilarious line, most often just from passing time with her. This post highlights a few of them.
Some of the details on who likes what presents (full descriptions here). Fujisaki's into punk rock. Togami likes the game where you play a wrathful smite-happy god as well as the underwear made for those with nice derrieres. It's possible to troll everyone with presents they absolutely hate. Then there's the Yonkoma where Naegi spams Celes with rose whips until she wonders if he's insinuating something.
In the new set of free time "trips", Mukuro Ikusaba has an increasing amount of trouble keeping her secret, as she absently lets slip details like her camouflage suit and her knife-throwing skills. Backpedaling follows.
Naegi: Do you know how to cook?
Enoshima: Well... I know how to build a fire to heat up rations. Er-! What I meant to say is, I make a mean beef stew!
A possible exchange on a "trip" to the dining hall:
Kirigiri becomes pretty competitive when Naegi challenges her to a game of Othello.
"But to be so cavalier with your invitation... Do you think you stand a chance? I won't go easy on you, you know. I'm not a big fan of losing. But you should know, Makoto... your face always reveals what you're thinking, plain as day."
She also goes into thought over the implications of the chicken coop's presence.
"Indeed, it's a chicken coop. But who's been taking care of them? It would be difficult to get them to breed without at least a little help. It couldn't be Monokuma... could it? Why would a bear bother taking care of a bunch of birds...? Hmhm, I must admit, the thought is rather funny."
The default ending. Possibly with a side of Fridge Horror, as the students all leave alive but appear to have no idea what happened to the outside world.
Syo: Oh, how good of you to realize! The truth is... if I donít constantly drench my tongue in fresh blood... Iíll end up dying! Such is my fragile life! Because I was born with such a condition, I was forced into the tragic fate of repeated killings...
Syo:... like hell thatís true, dumbass! If it gets dry, Iíll just use the sprinklers here or some shit.
The second Monokuma backup: the Monokuma Entertainment System. More accurately: the Monofurby. Upon being booted up, it immediately claims that its life is a travesty and, upon being smashed by Monokuma, yells "Sweet release!"
Looks like the MES is blasting off...again?
The back-up for Monokumadult is plenty amusing.
Monokuma: Huh? This thing looks just like me. Wait... what's this on the back? A zipper? And... is that a voice I hear coming from inside?
(banging noises) Help me... Someone... help me...
Naegi: (I think I just heard something I don't think I wanted to hear...)
Monokuma: ... Listen, is everyone present and accounted for? Nobody missing? Okay, just making sure...
(more banging noises)
Monokuma: I guess I'll just pretend I didn't hear anything!
The gift of underpants following a character's School Mode ending is pretty funny, but Junko Enoshima/Mukuro Ikusaba's is particularly hilarious given her unique background. It's plain, durable, bullet-proof and blade-resistant... but apparently not spear-proof.
When one thinks about it, the fact that it was the students themselves that put together all those dysfunctional Monokuma models, culminating in a replica of Usami. So it was someone's idea to build multiple bickering heads to "multitask", the Monofurby, solar panels for the Ecokuma when they're shut in the school with no access to sunlight... And considering a number of them talk and possibly have rudimentary AI, maybe Fujisaki is more of a smartass than we thought.
In Fujisaki's ending, he finally reveal that he's a guy but Makato assume he's joking. What Fujisaki does? Force him to touch that certain place. No not where Sakura touches but Fujisaki force him to touch his chest.
Monokuma dancing in the opening song. It's been compared to the dancing girls in the opening credits of James Bond films.
Monokuma in episode 2 'portraying' some possible executions like electric chair, poison gas or slashing hurricane. It was very fun and you'd probably wish it happens FOR REAL to that little ***er...
During the first class trial Celestia asks who Oogami is because she has forgotten what she looks like, when Oogami introduces herself all sounds stops at once for a couple of seconds so we can absorb her character design.
The game also adds up how Asahina said that she invited Oogami into her room... and then there's still someone in denial:
Ishimaru: It IS a problem! A boy and a girl spending the night together!? It's... it's unwholesome!
Oogami: But... I'm a girl.
Ishimaru: Wh-!? You are!? Oh my gosh, I'm so sorry!!
Oowada and Ishimaru tell Naegi to forget about their "battle", because now they are bros. Then Ishimaru does THIS:
The opening to episode 4 in the Anime. Crack doesnt even begin to describe it.
Togami's facial expressions in The Animation are absolutely sidesplitting, particularly when Genocider Syo insults him and when he finds out Fujisaki is a guy. Not to mention how on certain occasions when he's insulted, he repeats the insult (i.e. "ugly glasses") in an apparent state of disbelief.
When Hagakure sees the Bloodbath Fever message.
Hagakure: It's a shining message!
Asahina: I don't think that's the right wordÖ
Genocider Syo explaining why she wishes she was the one who killed Fujisaki during episode 5.
Genocider Syo: (After Fujisaki's crossdressing has been revealed) Damn, that's freaking hot! I wish I killed him.
Episode 5's execution turns into Black Comedy when watching it on Hulu, because it can cut from Oowada being fried and turned into pancakes to a commercial where a family is being serenaded by The Flaming Lips as they eat pancakes.
In Episode 6 of the anime Hagakure can be seen giggling and poking the breasts of a Venus de Milo-esque statue.
In episode eleven, Naegi tries to wake Fukawa who is passed out on the floor, only for her to leap up and reveal that she's currently Syo with some cackles and flamboyant poses... and when we cut back to Naegi, he's just standing there, and says "Genocider Syo..." with the most bored, unaffected face. This is commonplace to him by now.
Episode 12 has Fukawa show the others her group picture, taken during the winter. Kuwata's adapting his baseball talents to rapid-fire snowballs against Oowada, Ishimaru, Yamada and Hagakure all at once, Togami appears to be giving orders regarding Oogami and Asahina's giant snowman-in-progress, and in the instant of the picture another snowball nails Junko in the face.
Very darkly funny, but during every one of Monokuma's executions, Monokuma deliberately inserts a humorous event into it. Chapter by chapter, here they are:
In chapter 1, after Leon Kuwata is executed, we get a montage of everyone having shocked faces at how cruel the execution was, and Monokuma's own shocked face appears in the lineup. Furthermore, Monokuma spinning a bat like a whirlwind with a baseball cap on is absolutely sidesplittingly hilarious.
In chapter 2, Monokuma begins Mondo Oowada's execution with his own copy of Oowada's "corncob pompadour" hairstyle.
In chapter 3, before Celestia Ludenberg can burn to death at the stake, Monokuma turns the whole thing into a ridiculous farce by sending a fire truck to put out the fire, complete with big honking sign shouting "Help! Help! Help!" and after the fire truck rams Celes to death, Monokuma puts out the one tiny remaining flame with a fire hose.
In chapter 4, as Monokuma is using a bulldozer to crush Alter Ego's laptop into a ball, we get some brief shots of Monokuma joyfully messing with the controls as though he's playing a videogame.
In chapter 5, the chalkboard professor-Monokuma is using to teach the about-to-be-crushed-Kirigiri-or-Naegi a lesson changes midway through. It starts off as a diagram of the crushing machine the conveyor belt is pulling them towards, but midway through the execution video it changes to a sexual education lesson on conception.
Pretty much any time Fukawa indulges in her one-sided S&M relationship with Togami is either creepy or hilarious (or hilariously creepy).
If you're the sort of person who compulsively examines everything in the game world, some of Naegi's interactions with the objects can be quite funny, especially if you keep checking them as the game progresses. Things to look out for include (but certainly aren't limited to) the school swimsuit in the laundry room, the pile of veggies and the deli counter in the kitchen, and the vending machines. Naegi also likes to snark about the ubiquitous monitors and surveillance cameras all over the school whenever inspiration strikes.
Naegi: *looking at the school swimsuit* Despite everything, seeing it still makes my heart beat a little faster. That feeling is eternal.
Naegi: *looking at the pile of veggies* Are these supposed to get me excited? What am I, some kind of hippy-dippy all-organic celebrity type?
In the manga, Celes's Imagine Spot of the surviving boys as her butlers. Naegi has a monocle!
A number of the wrong answers during the multiple-choice sections of the trial can be these. Examples include, but aren't limited to, claiming you knew Oowada was the culprit because you hate him, claiming that a pair of pants were the intended recipient of a note, and implying that some mysterious sneaker prints are the work of Kuwata's ghost.