When Jeff Daniel's character is cooking for his two sons and the son walks into the kitchen and catches his father putting their meal that fell onto the floor back into the pan.
Also when his son Walt walks in on his father and the young girl and you hear the father say "Put me in your mouth".
I read through all the responses to make sure I wasn't repeating anyone and can't believe no one said the funniest scene was that poor cat getting dragged back and forth between the two houses. Who has shared custody of a cat? No one! It killed me.
Also, yes, the scene with the desk the dad put in the boy's bedroom, and the kid said, well, I don't want a chalkboard and a bell ringing every 45 minutes either.
Most have been mentioned already, but I can't believe you guys didn't mention the headbutt scene!
Some other humorously tragic scenes:
the mother hiding the books under Frank's bed.
Frank going shopping and how the father reluctantly gives out the money.
Walt picking up the piece of paper roll from the trash.
The entire conversation where the father subtley tries to talk Walt into breaking up with Sophie and then talks about the "very sexy" groupie that came up to him after a reading, yet couldn't sleep with since he was with Walt's mother at the time.
When Walt is puffing himself up posing as an intellectual, dismissing everone else, just like his dad, and he says "The Metamorphosis is very Kafka-esk" and Sophie sweetly points out that it was written by Franz Kafka, so yes it WOULD be "Kafka-esk"!
So many scenes have some kind of great subtle humor in it, superb film. The kid singing Kyrie at the contest was funny but also demonstrated that was probably the level of competition Walt had and he would probably have won without lying and just performing the Pink Floyd song.