When the class was brainstorming for the festival, and Taisuke was suggesting things like "every girl who buys something gets a kiss from me", "I get every girl's phone number", and Setsuna replies "Denied" to each and every one of those with a straight face.
The Zettai Ryouiki scene. It was the last funny thing in the story before hell breaks loose, and it was funny due to the fact people are acting serious about NOT GETTING ENOUGH CUSTOMERS. YMMV
"Softcore Porn!" and "We have entered into a non-agression pact with Class 1 and 2" have to be some of the funniest lines in the series
Everything about Magical Heart Kokoro-Chan. Depends on your humor, however.
Makoto Lampshading himself in episode 8 by saying, "I'm the worst."
This might be a bit of a black comedy example: during the infamous sex scene with Kokoro in Summer Days, it takes place in Kotonoha's house, and Kotonoha is still in the house but she's asleep. She does in fact hear Makoto and Kokoro going at it and she briefly sits up, but she's half-asleep and doesn't understand what she's hearing, so she goes back to sleep. When Makoto is just about to finish, then Kotonoha finally puts two and two together in an "extreme delayed reaction", wakes up, and bashes Makoto over the head with a golf club. It's the "extreme delayed reaction" on Kotonoha's part that makes it funny, obviously, not the underage sex.
Another Black Comedy, during the music part in episode 11, Makoto goes over his cellphone. If you look at the cellphones, it contains all the girls he had sex with. The funny part is the last sex scene in the anime involved Makoto and a threesome. And if you count the names, the number goes up to 17. It could have been more people he slept with, but he stops at Kotonoha. So it was kind of funny since he manages to cheat a threesome and manages to sleep with 16 women.
Before that, she's seen chugging down a whole bottle of a drink which is said to have 40% alcohol. No wonder she was so plastered.
Kotonoha confesses to Sekai that Makoto might be cheating on her with another girl. Sekai is about to confess that he does it with her, but then Kotonoha takes out a knife and rants about how she wants to kill that girl, if she only knew who she was cue Sekai slowly getting away while crying in terror.
The scene at the pool, where Green Eyed Sekai stares at Kotonoha's Gag Boobs, asking "are they real?", and after confirming it with a poke (to Kotonoha's amusement and mild embarrasment), mumbles in defeat "they are real..."
A hilarious misunderstanding between Otome and Makoto on the day of the festival. Makoto tries to ask her to get those Two Girls that hang out with her to man the registry on their shift as they were supposed to, rather than force Kotonoha to do it during her time off. Otome at first she thinks he is in love with one of them, and then thinks he wants to sex them up either one of them, or two at the same time and wants her to ask them for him. Even after the misunderstanding gets cleared up, it's still funny in a karmic justice sense, as Otome's Posse Girls sit behind the registry arguing, while Kotonoha and Makoto go to walk around the school for the festival.
Nanami complaining about her boyfriend Kyouichi ignoring her advances because he is playing a H-game (in-universe), and Hikari's and Setsuna's reactions.
Makoto comes across Taisuke and Kotonoha at the train station, and they seem to be having an argument of some sort.
Taisuke: That's not what I mean! Our trains go in opposite directions, so we have to split up here.
The With Kotonoha ending. It starts with Kotonoha lying next to a POV Makoto (clearly post coitus). They talk for a while when Kotonoha's cellphone rings. He answers it, but accidentally hits the button to use the camera. Cue Kokoro getting an eyeful of Kotonoha naked, complete with cries of distressed horror. Makoto, you're in big trouble now.
Makoto:Ah! I've really done it now.
One of the endings of Cross Days consisted of Yuuki ending up with Roka while punishing Makoto at the same time, with him and Ai being interrogated by Kotonoha about who's the father of Ai's baby. It's Yuuki. The fact that the music is extremely funny while Kotonoha draws out a katana, in one of the few times when her Yandereness is Played for Laughs, makes it even funnier.
Shiny Days's opening itself is rather funny. First you'll spot the usually calm and serene Youko making a super pissed-off face. Then you will spot an angry Setsuna and Makoto nearby having Imagine Spot of Futaba, Kazuha, Kokoro, and Youko with hearty background, but Setsuna will explode when it contains Karen's kiss blowing at him.
The Son-in-law's Ritual Ending in Shiny Days is quite funny. Makoto is allowed to court Otome and Karen, but not before being beaten up.
In Shiny Days, Hikari gets aroused by watching a certain couple go at it outside. What makes this hilarious is how a horrified Makoto looks at Hikari as if she had grown two heads or something.