Tony Shalhoub speaking gibberish is a direct spoof of his role in Quick Change (1990) where he plays a cabby who speaks gibberish.
One of the first episodes where Stottlemeyer actually starts thinking like Monk in solving a crime (about the worker).
Benjy is reading The Amazing Spider-Man #43 (September 2002).
When Darryl calls on the phone and asks if the person answering was Sharona, Gail responds with "No. This is her younger sister Gail." In real life, the actress who plays Gail, Amy Sedaris, is 7 years and 4 months older than the actress who plays Sharona, Bitty Schram.