Episode 3 has Death the Kid freaking out over every little asymmetrical thing. Later, he storms the pyramid only to find the evil Pharaoh has captured Patti and Liz with his tentacle-like bandages and is apparently molesting them. Kid blushes and tries to leave, saying, "Didn't mean to intrude..." until Liz yells at him to save them.
During Episode 5's fight with Stein, Black☆Star really takes a pounding. For the people who don't like him, this is great enough, but there's this downright hilarious line:
Stein:*kicks off with his swivel chair, simultaneously defending himself from Maka and attacking Black☆Star* Black☆Star: OW MY FACE!
Also in episode 5 was Lord Death's description of the bond between meister and weapon as a guitar and an amp. In the background, Maka's strumming on a guitar gently with a smile to demonstrate the meister on their own, then plugs in the amp and starts thrashing on the cords while Soul looks on to show what happens when the two of them work together.
Episode 7 provides a moment of levity midway through, when Spirit tries to seduce a DWMA nurse... only for it to turn out to be Dr. Stein coming in the door. Not only is his reaction completely hilarious, Stein convinces him that he swapped his toes around. However, the delivery of the last line of the exchange is what seals it:
Stein: Made you look~
In episode 8, when Medusa (who at this point is still the school nurse) comes into the infirmary, after greeting the kids she asks Maka, completely calmly, "I wonder if you could pry off your father, who's clinging to my leg." They look down and see Spirit clinging to and rubbing his face against Medusa's leg, loudly trying to hit on her, with glowing pink hearts around him. Maka delivers a well-placed Maka-Chop and the next shot is Spirit lying in the hospital bed next to Soul, with a nosebleed.
Even better is how Medusa is smiling and not reacting to maintain her cover, but she's definitely thinking, "So help me, Maka, I'm going to kill this idiot in two seconds if you don't get him off me."
Every time Stein falls off his swivel chair. Every single time.
Episode 13: As part of a bonding exercise, Stein asks Soul and Maka to list each other's faults. Soul immediately gives out several, including saying she's boring because she reads so much, and ends with "And you have fat ankles."
Her slapstick reaction adds to the comedy gold.
Chapter 12/Episode 14:
Spirit wants to get Maka a gift to congratulate her on being the best in her class, but is too embarrassed to give it to her in person. So, he has Blair get her something, hinting that she likes books. However, he doesn't anticipate that Blair would be lost to temptation, and ends up buying something for herself instead. She decides to change the size of it and give it to Maka anyway. What did she buy? Skimpy lingerie and a copy of the Kama Sutra.
It's harder to tell whose reaction is funnier, Maka's what-the-hell face, or...this:
Soul:[holding up the underwear] Wow...It's so transparent I can read the calendar on the wall through it...
Oh it gets funnier. See, Spirit included a note with that gift telling Maka to relax and have fun with it. Now Maka thinks her dad wants her Innocent Cohabitation with Soul to stop being so innocent.
The entire testing scene. Kid's reaction to not being able to write "K" and then ripping the paper is to shoot a burst of blood from his nose and mouth and then pass out on the floor. And Patti with the giraffe. Funnier when Patti actually got a 2 on the exam "because her art was done so well."
You can't help but feel sorry for Soul after he gets stripped down his underwear (as he hid all his notes in his clothing), but seeing Black☆Star pinned to the wall by his shirt using some of the blood from his nose to sign his name on the wall beside him and then give a thumbs up to Soul, who doesn't appreciate the lack of help.
Kid getting annoyed because he got smashed into the side of the ghost ship and then demanding that they crash into the middle of the ship, which ends with him smashing into the ship again.
In episode 16, Kid is chasing Crona and Ragnarok on his skateboard, and has almost caught up to them...when he notices how the sun and clouds are perfectly symmetrical. He completely forgets about catching Crona, and immediately turns around and rockets off towards the sun, ecstatically shouting about how wonderful it is.
Kid: Oh, sun! Oh, clouds! I LOVE YOU!
Even better, Kid actually stops and notices that Crona's getting away, then a second later he decides to ignore it and keep speeding towards the sun.
Crona's confused "Huh?" when Kid suddenly goes the other way just adds to it all.
In episode 17, Black☆Star's report on Excalibur consists of only his signature and the word "FOOLS!"
Medusa getting dragged off by Stein to dance in episode 18.
Ragnarok does a real funny line in episode 19:
Ragnarok: Hey, did something with four wheels, two legs and two arms just blow past us?
Also from episode 19: The Mizune sisters are destroying Death City and killing people left and right, and all Blair's worried about is that she's bored and has nothing to do. She thinks the explosions all around her are just part of Shibusen's party!
Episode 21 has Kid do one of his usual breakdowns and Liz is sick of trying to cheer him up.
Liz: [sigh] It's your turn Patti. Tell him in that special way that you have. Patti: Oh, okay. [shuffles demurely for a moment] Get your ass moving now, damn you.
Despite being a sad scene where little Maka erases little Crona's sand circle, she way she says "All gone" and the long silence that follows is sure to raise more than a few giggles.
Black☆Star meeting up with Kid in episode 22 had this troper almost in tears. Also, all of Kid's breakdowns and then subsequent snapping.
Maka succumbing to the black blood and going batshit crazy on Crona is pretty much horrifying...until she tries to eat his/her head, at which point it manages to turn funny for a moment.
Maka being completely confused about playing basketball.
Maka: W-wha? What did I do? What's a "double dribble"? I mean, it sounds kinda cool...
Maka having to ask her dad to spend a whole day with her as punishment for losing a basketball game. She reluctantly asks, and everything is silent for a few seconds... and then his HEAD EXPLODES.
Maka tries to get Crona out of his/her shell by taking him/her on a tour of DWMA. Fun Size Ragnarok is not amused, so he tries to piss Maka off by... lifting her skirt. What follows is a truly epic Maka Chop—which he blocks by using Crona as a shield. Poor Crona.
Crona's poetry. Everybody who reads it is immediately banished to "Mr. Corner" wishing they'd never been born. Gets funnier when Sid (who was throughout the episode sad that Crona was scared of him) randomly appears in the corner out of nowhere, wishing he never came back to life. Now, keep in mind that in the people who ended up in the corner, there was: An experienced Meister, A Death Scythe, several Living Weapons, a god-damn ZOMBIE (and Weapon Meister), and a few students who regularly fight unholy soul-eating monsters. Apparently that was one BAD emo poem.
And there's Soul's reaction to Sid randomly appearing in the lineup:
Sid: I wish I'd never come back to life...
Soul: What the hell, Sid?! When did you get here?
This exchange from episode 27:
Arachne: Giriko— Giriko:[angrily]WHAT DO YOU WANT, LADY?! Arachne: I detest children who shout. Shouldn't you know that by now? Giriko:[instantly pleasant and polite] How can I help you, ma'am?
In episode 31, Spirit has to mimic Lord Death to Justin since Lord Death's mask prevents Justin (who's always blasting music in his ears) from reading his lips. Spirit thinks he can get away with summarizing the Grim Reaper's somewhat-long sentences.
Lord Death: Hey! That's not what I said! Repeat it properly from now on. Spirit: You're taking too long to explain it. Lord Death: Say that again. Spirit: Yeah fine, I got it.
With that, Spirit not only copies each sentence perfectly, but he even perfectly mimics Lord Death's voice and mannerisms!
Episode 29: Stein has Maka, Soul, Black Star, Ox, and Harvar fight him in class in order to help them learn to resonate as a group... only to watch them utterly curbstomp themselves thanks to Maka backhanding Black Star into a wall with Soul and Ox accidentally going Royal Thunder on Black Star's derriere instead of Stein's. Twice.
Black Star starts the fight by leaping at Stein and yelling, "DIE, YOU GORY MOVIE REJECT!"
Later in the episode, Giriko and Mosquito get in another one of their arguments and start beating each other up, destroying part of the dining room. While this is going on, Arachne just sits there and keeps eating, not giving one fraction of a fuck.
In the anime, Rachel's mother opens a window to try and get Arachne's spider out (before Rachel!Medusa crushes it). In the manga, though, she tries to hit it with her husband's porno magazine.
Death keeps mockingly picking her up by her hood, and she pitches a fit every time he does it.
Then there's the part when Spirit and Death are discussing how to properly layer a joke, and Medusa is slowly backing away from them with a completely blank face. Even funnier, she's balancing on her snakes as she does this.
From earlier in the episode, Medusa's unimpressed expression when Spirit brings her into the interrogation room, and the fact that there's a sock on the rack of torture tools. Before that, there's Medusa's attempt to pull Deliberately Cute Child on Spirit to get him to talk to her.
When the team infiltrating Arachnophobia's headquarters by Dressing as the Enemy are involuntarily split up, Soul and Kid end up in Angela's room. Angela is invisible except for her hand holding a switch, but they have to pretend she entirely invisible. She whacks Soul in the groin, then Kid dramatically sheds a tear while telling his fallen comrade he will be joining him soon, praying that Angela at least hits him in the exact center.
In Chapter 62, Stein comes to Lord Death with definitive proof of the identity of Buttataki's killer. Of course, since it's Justin, and the evidence is an audio recording of his confession, the whole thing is drowned out by Justin's extremely loud music.
During his fight with Mosquito, Kid's Defense Mechanism Superpower enables him to fire a mass of shots at once at the vampire's 'legion' of bats. Kid's reaction is typical:
"If you're going to fly, then line up and fly in an orderly fashion!"
In Chapter 63, Death the Kid rearranges all the bookmarks in the book of Eibon when Noah isn't looking. If he's to be imprisoned in the thing anyway, it should at the very least be organized in a tidy fashion.
When investigating one of Medusa's old labs, Patti finds an eye and the jar and decides to challenge it to a staring contest.
The scene where Justin tells Tezca that he can't lipread what he's saying because of his massive bear mask. Tezca's reaction is hilarious when he realizes that someone he considers his friend has never understood a single word he's ever said.
Nearly all of Chapter 69 is one. The scene with Justin, Medusa and Tesca Tlipoca that goes into a Overly-Long Gag stands out, Black☆Star threatening to eat Eruka in her frog form, and The Stinger with Death the Kid were all hilarious.
Chapter 74: Excalibur suddenly shows up in the Wrath chapter of the Book of Eibon after not being seen since volume 9's special chapter. Black☆Star is not amused. Then just when they all thought they got rid of him by going to the next chapter..."NOT AGAIN!!!". He's disposed of when Liz uses him to create a rip in space and then tosses him in it. Even The Faceless makes the annoyed "I just met Excalibur" face.
Also beforehand, in one of Excalibur's rants, he's annoyed why he's put on the Wrath chapter when he thinks he's supposed to bring joy. Then he continues with the so-far anime-only "Excalibur Song" (I'm going to Californiaaaa~). THIS is what makes said Faceless make the annoyed "I just met Excalibur" face.
Also counting from Chapter 74 is the confirmation that Tsubaki and Liz are the team's biggest pervs. Besides Blair, of course.
In chapter 97, Eruka hears a voice on the other side of her prison cell, who reveals that it's Free, and that he's apparently there to break her out since she did the same for him. When she opens the door, Free is also in handcuffs.
"Oh. You got arrested too, huh?"
Maka and Black☆Star are talking while in the sky, but then Black☆Star suddenly loses altitude and he regrets how his scarf pole-vaulting has damaged several houses already.
Kid is in a rush to talk to the Witch Council about combining forces to save the world from Asura, but it turns out Kim (who he needs to get there) is in the shower. His solution of course it to rush into the shower holding a sponge and try to help her clean herself faster. And we have Liz and Patti turn up and apologise for Kid being...Kid.
And she is glaring at him in the Death room shortly after.
Stein: One of the teeth just fell out... what in the world is happening on the Moon?
Maka, , black blood-crazed, comments on her own flashback while impaled on Asura's arm.
Soul's casual response to his and Maka's new black blood transformation.
Asura's comments about Kid being a new shinigami.
Stein throwing Marie to the moon which leads to Marie missing her target by 'quite a bit'...only to manage to turn around and smack Asura anyway.
Chapter 112: Maka is in the middle of telling Crona about The Power Of Trust, then uses the weirdest choice of words possible:
Maka: You believe in me too! Almost like a stalker.
Earlier, Crona assumes that Maka's a hallucination. Maka responds by giving Crona a Maka Chop. This proves to Crona that, yes, Crona is seeing the real Maka.
The sheer audacity of having the final chapter be about boobs. Lots of them.
Also, Excalibur interrupting Kid's requiem speech for his father by talking about food.
While Kid is talking about the Madness of Boobs take a look at what the moon looks like. Real subtle Ookubo.
Kid and Spirit during the Awesome Moment of Crowning. Apparently it took a few tries to put the mask on the way Kid wanted.
The bonus chapter where Hero manages to wield Excalibur (not even having a problem with his 1000 rules) and then terrorizes the Academy. In the end, not even he can stand Excalibur when he starts sneezing over and over again.
Excalibur also interrupts his own monologue to just stare right at the viewer, his face getting bigger and bigger in every panel until it takes up an entire two-page spread. Nothing happens after that (except Black☆Star getting really pissed off.)
Maka mentions that her mother travels around so much that she doesn't even know where she is most of the time, and Crona of all people gets an aside questioning her parenting skills. Crona asks her what her favorite memory of her mother is and Maka cheerfully mention it to be when she divorced her father.
Crona: What a weird answer. Maka's got a strange family life...
Shinigami activating BREW, causing Death City to sprout limbs and become a Humongous Mecha. Naturally, the enemy stronghold does the same so they can have a giant robot duel. In the ensuing battle, Shinigami not only uses Death City Robo to execute his signature chops, but also delivers an Eye Poke technique at one point.
Afterwards, it grabs the Kishin and eats him. Cue this troper's jaw dropping due to the sheer insanity of that scene.
Not to mention the Death City Bot's special attack: COFFEE TABLE FLIP!!!!!!!
The look on Maka's face when she sees the Death City Robot.
The Where Are They Now epilogue during the credits also has a few funny moments including:
Marie and Asuza taking Rachel back to her family, and Marie dotes, over the happy family. Asuza then says something that causes Marie to "Marie Chop" her.
Joe, dancing in joy with his favorite coffee shop opening up again.
Crona's terrified reaction with playing basketball with the protagonists, especially with Maka coming at them.
The improv skit at New York Anime Fest as a whole could count as this (being based off the same fight in episode 6), but Todd Haberkorn manages to stand out when he (quickly) gets tired of imitating gunshots...
Kid: Gun! Gun! Gungun! Gunning! Gunning more! Gunning two times! Symmetry is awesome! Gun!
At the end of chapter 88, Marie announces that she has news on Crona to the group. However, one scanlator included a translator's note above a panel of just them from behind, below the waist.
(directly over Soul, with Tsubaki to Soul's left) That ass!
Some of the character's comments on their rank in the second popularity poll are quite funny, but Crona's may be the best: