Tomoya: "Why? You've got to be M, Kawai-san! You're bigger than me!"
Maria: "No, I'm S."
Tomoya: "You should be M! Kawai-san is M!"
Maria: "S is more suitable!"
Oh yeah, they are talking about clothing sizes. Probably.
In the Amatsuki manga, this troper found it particularly hilarious that (although it was already laden with plenty of puns and typical manga style reactions to everything which, while amusing are still pretty cliche and boring) when the manga finally started to get down to something plot-related and serious, Thisexchangeoccured.
The entirety of the H-manga Sei Sou Tsui Dan Sha is either one of these or horror depending on your point of view, but the very end is an unquestioned, one-wordFunny Moment. "MOM!"
In the Tengen Toppa Gurren Lagann manga rendition of the hot springs episode, the heroes discover that the spring they've been bathing in is really part of a giant enemy Ganmen. The fanservice girls are scooped up in a cage, their... delicate parts obscured by blurry pixels, with the enemy threatening to kill them if Simon and Kamina does not surrender and step out of the Gurren-Lagann. Kamina's response? Sure, "as long as you remove those damn blurry parts so I can see what I think I'm seeing!" They do. The girls were wearing bikinis all the time. Kamina is not pleased. (Neither are the girls, for that sake.)
This is, in fact, in the uncut version of the episode. Twice.
Leon at the end of the Pet Shop of Horrors manga. "I can't believe it... I'm really flying! That means... I'M FUCKING DEAD! THAT LYING SACK OF SHIT!"
So many from Great Teacher Onizuka, but one in particular sticks out in memory to me. During the Okinawa trip, Urumi realizes that Onizuka has been using the class as cheap labor to help him search for treasure. Getting Urumi mad at you is a Bad Idea. She buries Onizuka up to his neck and then covers him with huge snakes and giant beetles. This troper laughed hysterically for several minutes.
The Hentai manga Bondage Fairies prides itself on its humor. One of the best would have to be New Chapter 3, when Elder Granny has to decide, between Pfil (the innocent and joyful one of the two main characters) and Takapi (a side character who is arrogant and scornful of the main heroines), who gets the "honor" of being the Chosen One to "appease" Titanos the dread killer cicada of legend:
Elder: "Hrmm! Takapi is better!"
Takapi: "Heh... A wise decision. From each fold of my labia majora, to the delicate lines of my inner petals... I am beauty perfected!"
Elder: "No, you've just been stretched wider."
Pamila: (falls over laughing)
In the chapter of Shugo Chara! where Tadase tells Amu about his sad past with Ikuto, all the guardians seem to be depressed from hearing it. Until Yaya character changes and tells them to stop being sad and actually try to save Ikuto. How her face looks when she says it is downright hilarious.
The Pokémon Mystery Dungeon manga Ginji's Rescue Team. We're introduced to Absol, who, soon after meeting them, sees Ginji's identifying mark, an x-shaped scar. Cue him freaking out and eventually telling Mudkip that he's scared that Ginji will eat him.
I raise you the meeting with Xatu! When Mudkip and Ginji meet him, Xatu silently stares at the sun without acknowledging their prescene. Ginji gets p’oed and “accidently” uses Flamethrower on the psychic bird, who doesn’t react at all. Ginji and Mudkip are amazed by his intense focus. Then Xatu finally turns and questions who they are- and a second later starts screaming in pain! “Delayed reaction!”
"One never knows when she will appear next, or where!! I beg you, M'lord, to have her choose her partners at a proper audience, as is the custom, instead of snatching my men as they go about thier work!!"
Volume 4: Kyoko buys a full length mirror for her bedroom, and she wants to try it out by dressing up. She comes across her old high school uniform and puts it on. Mrs. Ichinose barges in to invite Kyoko over for drinks, and decides to put on her old high school uniform too. Yotsuya puts on monk's robes, Akemi puts on a nurse's uniform, and Godai puts on his high school uniform. The drinks come out and everyone starts playing parts according to their costumes, hamming it up and getting melodramatic. Finally, the kid, Kentaro comes home — and is heartbroken because he thought at least Kyoko was "kind of normal, at least." The chapter ends with Kentaro dreaming of moving out.
Volume 5: Godai and Mitaka are both in the hospital with broken legs. They're both pining after Kyoko, and she's trying to figure out who she has feelings for. Cue a harem of girls who come into the hospital to dote on Godai and Mitaka, so Kyoko leaves. Godai and Mitaka look out the hospital window to see her smiling—much to their relief—but she takes her umbrella and writes in the snow, "Idiots!"
Mirai Nikki is usually a very serious manga, but one quote from one of the later chapters doesn't fail to get a laugh.
The village of people who periodically encase themselves in a kind of jelly dessert which I've forgotten the name of.
In keeping with the extremely dark and twisted humor of the series, at one point in Ichi the Killer, after Kakihara tortured one of the conspirators for information, the necrophiliac man requested that after his death Kakihara fuck his corpse. Kakihara agreed to the request before driving one of his signature skewers through the man's brain. Then he stood up, turned to one of his unfortunate underlings, and said "Fujiwara. Take this guy into the bathroom and fuck him." And he meant it, too.
In Mega Man Megamix, uber-serious Elec Man busting out into laughter at Roll chasing Cut Man so she can make repairs on him.
From the same manga, this troper admittedly believes Metal Man got a Funny Moment when he insisted he wanted to fight more, whether that was an intentional Funny Moment or not. It doesn't help that in this troper's head he sounded like a whiny teenager.
Mega Man Gigamix Volume 2: Roll stuffing Shadow Man down in the bike basket.
The fight between Jack and Sikorski in Baki the Grappler takes place inside a telephone booth, where the cramped conditions make their size difference irrelevant...but there's a person in the booth trying to make a phone call when they do it.
In GA Geijutsuka Art Design Class, playing with a sweets container as a luxury liner ("That's actually the Titanic.") and being shown that the container readily returns to its shape after being bent: