Naegi's epic pratfall after Monobear interrupts his Moment with Maizono.
I aimed at Monobear, 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.
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 cleaning up after themselves:
Celes: Maybe you cleaned up to erase traces of Maizono-san visiting your room... ...isn’t that also a possibility?
After it's revealed that Sakura 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. Sakura 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, Monobear 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. Monobear snaps that there is no accomplice! Oops...
In chapter 2, 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.
Speaking of chapter 2, 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.
Also in chapter 2: Ishimaru and Mondo have a will power 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 the wrong kind of royal milk tea...
Celes: (cute smile) I only drink royal milk tea, in which milk is used to draw out the flavor of the black tea.
Yamada: Don't be so...
Celes: (completely pissed off) Shut up and bring my goddamn tea, you swine!!
Genocider Syo is a goldmine for these; using Makoto as a punching bag during a Relationship Values moment, and describing Togami's underwear with a Godot quote come to mind.
Their rant about how they can't be the culprit. The very last reason they give? She doesn't know how to make tight knots.
Their extended analogy comparing murders to ramen.
From the Zetsubou Translation: Kiyotaka and Mondo's breakfast scene has them ramp up the obnoxiousness by replacing their "anikis/kyoudais" with bro puns.
Kiyotaka: You're wasting your breath, Broseidon... a woman could never understand the depth of two men's bonds...
Mondo: Well said, Broski... mind if I get a tattoo of that somewhere,
Kiyotaka: 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 [X] was the culprit. The player gets to answer for her, and one of the options is "Because I hate [X]."
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 Sakura volunteering for the task and roaring in shock when she finds out. Then the others react.
Yamada: Oh, I see! She was a man! Thank you very much for your troubles!
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 can’t even bother to open Google and search for things themselves?!
Togami's reaction to Monobear's bribe.
Naegi: A figure like ten billion yen... that's...
Togami: ... way too little.
The scene where the others find out that Yamada's developed a... thing for Alter Ego.
Hagakure: There was a certain CEO I gave spiritual advice to that one time... He fell in love with a mannequin, and even went so far as to have a wedding reception with it. Your eyes, Yamada-chi...! They’re just like that CEO’s were!
Yamada:(shouting) Stop it! She’s not a mannequin! She’s an angel!
Yamada:(composed) Whether angels really exist or not is a separate question. Please suspend your disbelief for this.
Followed shortly by:
Yamada: I love her face and her personality and the way she talks and her keyboard...
The picture of the 'strange person', and the nonplussed reactions it gets out of everyone.
And later in the trial when they were discussing on what the two people in the photo were actually doing, two of your options were "They're drunk" or "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: Don’t put that virgin and me in the same group! His virginity will reflect on me!
Hagakure: I don’t think it’s as much a reflection as it is that you are one, ‘right...?
Asahina:(taken aback) Wait a second, are you saying that kind of thing is that easy to tell?!
Celes:(smiling) ...Please let us not continue this unseemly conversation, and just enjoy breakfast.
Togami's response to one of Syo's romantic propositions.
Togami: You’re not making any sense...
Togami-kun finished talking, slowly turned his body around...
...and then unexpectedly took off with a sudden burst of speed, sprinting out of the cafeteria.
Earlier, the revelation that Togami's hiding out with a stack of books in the pool changing room.
Genocider Syo announcing their 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 underpants 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 "[Dead guy's] underpants." And then when he gets a question about something two people both did, one of the options is "Hiding a note in their underpants."
Hagakure 'attempt' to try to dodge Celes' accusation that 'Yasuhiro' refers to him.
M-my name is n-not really Yasuhiro! M-my real name is actually, um, Tarosuke... or something...
Even better? The only one who's not that far away is Kirigiri.
"Gra! Give me all your donuts!"
At one point in the final trial, Monokuma's shouts out two of Nihon Falcom's titles successively as an Oh Crap reaction, which is Xanadu and Faxanadu. Even better? Those lines are voiced.
Monobear calling Celes "Celestia What's-Her-Face" (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.
"Who the hell are you?!" "Ah, I'm the mastermind." "Nice to meet you!" "Nice to meet you too."
Even better are their expressions. Genocider Syo passes from "pissed off" to "Nice to meet you!" in an instant, while the Big Bad is depressed and has mushrooms sprouting from her head.
One of the pictures that Monokuma gives the characters showing their school life before their memories were erased includes Sakura pulling a Shoryuken on an inflatable shark with Yamada thrown into the air.
Junko'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, Junko'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 either Kuwata or Sakura bursting out of the water with the aforementioned Shoryuken. This goes further in the anime, where in Fukawa's wintertime picture she's being smacked in the face by a snowball
Free Time Events
Hagakure's first scene in his social link has this little gem when he attempts to predict Naegi's future:
Hagakure: Your child and my child...will share the same mother!!
Naegi: No! I will never allow it!!
Want to know something funnier? Make the wrong choice and this ends up happening at the end of chapter 5.
And in his last scene he asks for Naegi's kidney, or failing that his citizenship.
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): That's not something one gets wrong!
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: ...Welcome home, dear. Do you want dinner? Should I prepare the bath?
Naegi: Asahina-san... I think that's more a housewife than a girlfriend.
In one of Leon'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 Leon 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 Mondo asks whether Naegi prefers cats or dogs, he can Take a Third Option and reply "Bears." Mondo is not amused.
Naegi manages to keep Ishimaru from confiscating his trendy hoodie by claiming the hood doubles as a safety helmet.
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.
Monobear dancing in the episode 2's opening song.
Monobear 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 Sakura is because she has forgotten what she looks like, when Sakura introduces herself all sounds stops at once for a couple of seconds so we can absorb her character design.
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.
When Hagakure sees the Bloodbath Fever message.
Hagakure: It's a shining message!
Asahina: I don't think that's the right word…
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 Humor when watching it on Hulu, because it can cut from Mondo 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.
Your mileage may vary on how much this example is "funny", but during every one of Monobear's executions, Monobear 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 Monobear'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, Monobear begins Mondo Oowada's execution with his own copy of Mondo's "corncob pompadour" hairstyle.
In chapter 3, before Celestia Ludenberg can burn to death at the stake, Monobear 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, Monobear puts out the one tiny remaining flame with a fire hose.
In chapter 4, as Monobear is using a bulldozer to crush Alter Ego's laptop into a ball, we get some brief shots of Monobear joyfully messing with the controls as though he's playing a videogame.
In chapter 5, the chalkboard professor-Monobear 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.
In chapter 6, usually, before the executions happen, we get an 8-bit "game over" clip of Monobear dragging the culprit away by his/her head to be executed. Before this execution begins, however, we get the same 8-bit "game over" clip, but this time Junko Enoshima voluntarily just stands up and walks away with Monobear. Then, she puts herself through all the previous executions, and humorously lives through all of them. She survives Leon's execution because she doesn't chain herself up and she manages to bat away all the balls at hyper-speed, she survives Mondo's execution because she's stoic while dizzy with her arms crossed and not turned into butter, she survives Celes' execution by meditating like a yoga master in the middle of a friggin' burning stake, she survives Alter Ego's execution by having her pigtails deflect the bulldozer, she survives the space journey because the rocket launches up and down in an instant arc, and...finally, just before the crushing machine finally kills her, she's not pinned to a desk by her hands, she's just hugging Monobear and smiling at the viewer while doing a "V" victory sign.
Pretty much any time Fukawa indulges in her one-sided S&M relationship with Togami is either creepy or hilarious (or hilariously creepy.)
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 claiming you knew Oowada was the culprit because you hate him and implying that some mysterious sneaker prints are the work of zombie Kuwata.