There is a Klingon Bat'leth from Star Trek on the wall in Master Zi's martial arts academy. This is one of six connections to the Star Trek franchise.
At the start, Monk's new personal assistant asks Monk to pay her personal expenses. Monk responds by saying he didn't pay Sharona's expenses and couldn't afford to pay hers. This might be a subtle dig at the fact that Bitty Schram (Sharona) was written off the show after holding out for a pay raise.
Mako, who portrays the master martial artist, is called "The Wizard" by Natalie. This is a connection to Conan the Barbarian (1982). Mako's character in Conan the Barbarian is "The Wizard."
Kathleen Mary Carthy, the medical examiner, played the crime scene tech in "Mr. Monk Gets a New Shrink (2006)" (S5:E7).
Sonny Chow was born on May 19, 1946 and died on January 7, 1998.