Whenever Neko, in her cat form, starts yowling. She's just the tiniest little kitten trying her hardest to look intimidating.
Yashiro's nonsense-spouting in an effort not to be killed.
Yashiro: But I'm innocent!
Kuroh: *points him to the video showing him clearly guilty*
Yashiro: W-Well, maybe I don't look innocent... but you know what they say, right? Don't judge a book by its cover! It's what's on the inside that counts!
At the end, when Kuroh closes his eyes in his usual cool and composed manner, the viewer realizes that Neko has drawn eyes onto his eyelids, making him look ridiculous. The background music even stops abruptly for comedic effect.
Episode 3: When Misaki and Rikio crash into Izumo's bar get in a fight and promptly get their skulls crushed by said bartender. After Misaki explains what he and Rikio were fighting about, he resumes fighting while dangling in midair. It's only when Rikio and Misaki apologize to the bar that Izumo clears up the misunderstanding.
When Yashiro's cleaning robot gets buggy and first mistakes his bag as trash, and when Yashiro tries to retrieve it, it recognizes him as trash and tries to throw him away too. This, however, turns out to have actual plot significance...
Yashiro explaining things he got from Kuroh as being from "his wife", with Kuroh threatening to cut out his tongue.
Yata and Kumamoto dramatically prepare to enter Ashinaka High School to find Yashiro - only to be stopped comically at the gate because they don't have passes.
The beginning of Fushimi and Yata's Drama CD - Fushimi was the interviewer and Yata was the interviewee, but the former ended up answering most of the questions for the latter, many of which even the latter did not know himself (e.g. his current height).
Episode 8: Seri drowns a traditional Japanese sweet with disgusting-looking red bean paste, making it look disgusting. She then serves it to Munakata, who doesn't want to eat it, but being the polite guy he is instead of out-right rejecting it he sets it aside when Seri's not looking. When Fushimi arrives Seri asks him to come sit next to them. Once Fushimi sees Seri's surprise dish he replies that he's fine standing where he is.
Radio Drama 2:
(At an arcade)
Yata: Which one do you want to play, Anna?
Anna: Which one... is red?
Yata: How about that one zombie game? There will be 'red' coming out once you shoot them!
Anna: I'll play that.
Totsuka: Anna's clothes have really complicated designs... Can I take a look?
Totsuka: O-OUCH!!! Yata, why did you hit me?!
Yata: Weren't you peeking under her SKIRT?! Are you a lolicon?!
Totsuka: I wasn't peeking! What a terrible thing to say about other people! I was just picking up the frills on the top! Don't imagine such weird things... Aren't you the one who's a lolicon?!