Turk's middle name is revealed by J.D. as Duncan. Turk denies J.D.'s claim that his father was a big fan of doughnuts.
In the scene where the Janitor digs J.D. over his love with Elliot, the Janitor compared them with "Ross and Rachel". They are the names of the two of the main characters in Friends (1994), in which Bill Lawrence was credited for writing one episode for. In that show, Ross holds a doctorate in palaeontology and Rachel is a buyer/personal shopper. In this episode, they are known as "Dr. Ross and Rachel from bookkeeping".
In the last conversation between Dr Cox (John C. McGinley) and Mr. Corman (Richard Kind), it is revealed that Mr. Corman's first name is Harvey. This is a reference to actor Harvey Korman who is most famous for The Carol Burnett Show (1967) among many other television and movie appearances.
The song playing over the final scene is 'One Thing' by Finger Eleven.
J.D. says "Nobody cares, Danni" in the same inflection he does to Sean years later in My Cuz (2009).