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The Big Lipped Alligator Moment (which is Kouchi's Imagine Spot) during Episode 6. That spells out what the audience think 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.
Episode 2 had a funny moment in an otherwise Uncanny Valley 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 exchange between Mei and Teshigawara after Kubodera kills himself.