Courteney Cox had suggested the premise of the show Cougar Town to show runner Bill Lawrence, her 3 episode arc on Scrubs was almost an audition to see if Bill Lawrence enjoyed working with her. He obviously did seeing as Bill Lawrence became the show runner for Cougar Town starting the next year.
JD leans on the fourth wall at the start of the episode by seeming to point to the on-screen ABC logo, saying "Huh, that's new" (this being the show's premiere on ABC), but it's then revealed he is commenting on the janitor's watch.
This was the first episode broadcast on ABC.
When JD references that Dr. Shalhoub wins everything, he is referring to actor Tony Shalhoub's many Emmy wins including when Shalhoub won a Primetime Emmy in 2005 for which Zach Braff was also nominated.
Courtney Cox is one of the main cast in Friends, the show which this show's main cast had referenced on several occasions.