Professor Layton and the Unwound Future/Funny

Penny Arcade, mentioned above, complained about having to sort out "some jackhole's insane chicken scratches." Puzzle 17 in Unwound Future has you do just that.
When Luke, Layton, and Don Paolo are escaping through an underground secret passage, which is too dark to see anything.

Luke: Ow! What did I just walk into?
Don Paolo: I don't know, maybe a wall?

When Don Paolo finds out Claire is in love with Hershel, he runs away crying. Into a river. And he doesn't notice.
Really, Don Paolo had a good deal of funny moments in this game. Another good one would be when he lampshades Luke making an overly obvious remark by outright calling him Captain Obvious.
They dedicated a cutscene to revealing who Granny has sent to take over her job. Surprisingly not the bee we've been dealing with. It just pops out of nowhere and that it's an actual cutscene...
- Especially Puzzlette coming out of nowhere and swatting Beasly, right before he tells his story.
A simultaneous Moment of Awesome and Funny, when the Laytonmobile starts flying, we get this:

Luke: Wow! We're actually flying! Can you believe it?
Layton: Yes, Paul[Don Paolo] was always very good with machines.

Luke: Um, Professor? Just when did you learn how to fly a plane?
Layton: A plane? This is an automobile!