In episode three, three characters have a conversation in front of a fountain in the shape of a cherub... with water coming out of its butt. And the water pressure keeps changing, from a dribble to a spray.
Also in Episode 3, Yuuji appears at the movie theater being dragged by his (Hitherto Stalker with a Crush) girlfriend in shackles. She calmly informs him that they'll be watching War and Peace, The Movie, which runs seven hours and four minutes. Twice. And if he gets bored he can "sleep on her shoulder" - and she holds up a taser. And tases him mercilessly. And proceeds to buy "One student ticket and another unconscious student ticket for two runs." Slapstick is funny!
And in Episode 5, when the boys accidentally uncover a basket of small chiffon cakes that Himeji made, except that there are four boys and only three cakes at the time. After engaging in "Rock, Paper, Scissors" to determine the survivor, Voyeur is gagging on a cake, Yoshii and Yuuji are trying to shove a cake down each other's throat, and Hideyoshi is curled up near a wall, traumatized by the whole event.
Manga was funnier instead of eating said lunch after everyone collapsed he shoved it down an weakly struggling Yuuji because of the things he sent him through as revenge. Of course Himeji is none the wiser when coming back.
A better question would be to ask which moments aren't funny in this show.
In episode 10, the Smug Snake from class B gets his comeuppance when Yoshii leaves Himeji's cookies in his shoebox. This Troper bust out laughing out loud as soon as he saw the basket.
The sound of a soul being eaten away...
The FFF holds an "inquisition" for Akihisa when Himeji offers him some of her food, by literally putting him on a cross and sentencing him to death. When Himeji tries to speak up for him, all she can do stumble over her words before smiling cutely. They immediately set Akihisa on fire.
Shortly afterwards, in the very same episode, the FFF spot Minami trying to give her boxed lunch to Akihisa. She tries to explain the situation...only to also stumble on her words before smiling cutely. The FFF then resume their persecution of Akihisa.
Anytime Yuuji puts his hand on someones shoulder, seriously.
Akira: There's no way my dumb and ugly and useless brother would have any female friends. I'm guessing these two are male too.
Yoshi: Don't be so rude! You just screwed up everything! All three of them are female!
Hideyoshi: No, I'm a guy.
At the beginning of episode 13, Voyeur tries to look up Shimada's skirt for the first time in quite a few episodes. Doing so, he gets so excited that the friction he creates sliding around on the floor sets him on fire. He's okay, though, because it's put out by his own nosebleed seconds later.
Episode 7 of Ni!, Kouta is peeking out from under a blanket and slowly has a nosebleed that covers the mattress as he takes photos of the girls in the room. The bloody spot keeps getting bigger and bigger and after a shot of Hideyoshi the blood covers the whole floor.
Later on in that scene, Yoshi becomes alarmed over Ironman coming to their room, remarking how it would look bad since there are four half-naked girls there. Hideyoshi realizes that he was included in the four.
When Hideyoshi is introducing himself to the class, Minami thinks to herself, "I wonder why that girl's wearing a guy's uniform," ultimately deciding that it's probably because "she" doesn't like wearing skirts.
In Volume 7. Yuuji represented the class to negotiate with Ironman, going on a tirade about how education is important and all sorts of stuff. Ironman's response?
'''Tetsujin: "But I won't return those Ero-books back to you."
Soon after, the entire class of guys (note, no Hideyoshi), and went to fight Ironman. Ironman won easily.
Also in Volume 7. Class 2-F was going against class 3-A (note, the damned Toko-Natsu pair) in a summoned beast baseball tournament. The principal had enough of the boys trying to do collateral damage to each other (as each damage would hurt each other like usual summoning battles) and set every summoned beast's damage to affect the user as well (Note: Akihisa's Punishment inspector ability). Yuuji promptly placed Akihisa as the catcher and HIMEJI MIZUKI AS THE PITCHER. Given that the pitch speed would be equivalent to the points of the controller, and then Mizuki doesn't know and have any control of her baseball, and that the ball would be the equivalent of a weapon in a summoning battle, the end result was that 4 people 'died' tragically as a result, the Toko-Natsu pair, the batter who was supposed to be next, and their own teammate...
To top it off, the reason why Mizuki agreed to pitch was that Yuuji said that the pitcher-and-catcher relationship was a husband-and-wife relationship...
In Volume 10, Takagi's official introduction. Top of Year 3 in grades, bishounen, and an idiot who falls in love easily. Best of all, he got fooled by all the lies 2-F gave him. Keep in mind that this is the guy who came up with the plan that corner class 2-F in volumes 8 and 9. Oh, and he kissed Akihisa at the end of the volume
Any of the DVD specials. Seriously. These include: a fairytale retelling with Mizuki as Narrator (who actually acts as a Lemony Narrator in her favor) and the cast as the story's characters; a crossdressing pageant with Yuuko and Kubo as judges and the boys as contestants and the girls wearing the boys' uniform; and the King's Game, which has amazingly destructive results.
Episode 4, Season 2, especially the second half. The principal gets the main cast to test the trial summoning system, and Hilarity Ensues when the summoned beings act like children, speak like humans, and reveal their summoners' secrets...
Episode 8, Season 1, pay attention near the beginning when Akihisa is paying off Kouta. Kouta, for one brief second has a Geass
In the light novels, Volume 9.5, during their first day of school in Fumizuki. Yuuji meets Akihisa for the first time. Akihisa was wearing a sailor uniform. Yuuji immediately thinks he's a pervert.
In the first OVA episode, when Mizuki suggests a wedding coffee-shop for the school fest, the "demo video" shows Akisha and a bunch of FFF members with Wingding Eyes chasing after……Hideyoshi in a wedding dress.