Episode 2 had a funny moment in an otherwise creepy setting. Kouichi visits the doll shop for the first time and sees the doll that resembles Mei. The doll "speaks" to him, obviously freaking him out, but it turns out to just be Mei standing behind the display. What makes this more funny, was that he thought Mei was actually a doll to begin with.
The Big-Lipped Alligator Moment (which is Kouchi's Imagine Spot) during Episode 6—during a class exercise in which none of the students are allowed to move or speak, the two of them dance together in front of the class, since both of them are "non-existent" and no one is supposed to acknowledge their presence. That spells out what the audience thinks they will do if they were in his shoes. Doubly funny due to the nature of the rest of the show.
Speaking of which, Kouichi's facial expression when the scene cuts back to reality.
The exchange between Mei and Teshigawara after Kubodera kills himself.
The ferris wheel scene from the OVA. It starts with high dramatic tension with Misaki Fujioka dangling from the ledge, before finally having to be let go... And end in pure Bathos as she was already safely on ground level by the time she let go.
An unintentionally hilarious moment happens in the live-action movie, during the scene in which Sakakibara's introducing himself to his classmates. The rest of the class gives him unpleasant looks... except for one of the boys, who has a goofy smile on his face, as if he missed the memo on how his character's supposed to act in that scene.