In Mr. Monk and the Billionaire Mugger (2002), the psychiatrist in the hospital says that Monk is allergic to tomatoes, deducing that Monk was cooking Trudy's favorite meal for their anniversary. In multiple episodes since, including this one, Monk can be seen eating tomatoes, usually on sandwiches. Monk was very excited about the square tomatoes in Mr. Monk on Wheels (2009).
The gag during the bachelor party when one of the cops mentions to Monk that there is a bathroom in his bathroom (a port-a-john inside the bathroom) is a spoof of a story on 'The Onion' about a Starbucks opening inside the restroom of an existing Starbucks (which itself satirizes a common fact that one can find Starbucks shops practically next door to each other in major cities).