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 Ryouki 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 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 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.
In School Days HQ Visual Novel:
Drunk Setsuna, in ultracute mode, speaking gibberish and hugging Makoto.
Kotonoha confesses to Sekai that Makoto might be cheating on her with other. Sekai is about to confess that he does it with her, but then Kotonoha takes out knife and rants how she wants to kill that girl, if she only knew who she was - cue Sekai slowly getting away while crying in terror.
Scene at pool, where Green Eyed Sekai stares at Kotonohas Gag Boobs, asking "are they real?", and after confirming it with a poke (to Kotonoha amusement and mild embarrasment), mumbles in defeat "they are real..."
Hilarious misunderstanding between Otome and Makoto on day of festival. Makoto tries to ask her to get those Two Girls that hang out with her to man 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 in one of them, and then thinks he wants to sex them up, either one of them, or two at same time, and wants her to ask them for him. Even after misunderstand get cleared up, its still funny in Karmic justice sense, as Otome Posse Girls sit behind registry arguing, while Kotonoha and Makoto go to walk around the school for festival.
Nanami complaining about her boyfriend 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.
Makoto: What are you doing?
Taisuke: Having a goodbye kiss.
Makoto: You only announced you were getting together at lunch, and you're splitting up already? That was quick.
Taisuke: That's not what I mean! Our trains go in opposite directions, so we have to split up here.
One of the endings of Cross Days consisted of Yuuki ends up with Roka while punishing Makoto at the same time with he 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 Katana making it's even funnier.
Shiny Days's opening itself is rather funny. First you'll spot the usually calm and serene Youko making super pissed of 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.