When Gibbs places the evidence FBI envelope on the desk, the Bag Number is 8675309, as in Tommy Tutone's hit song "867-5309/Jenny I've got your number". The envelope contains information on a case involving the director of NCIS, Jenny Shepard. (Interestingly, the phone number of the song actually belonged to a family in Topsfield, Massachusetts, and caused the household to have to change all of the phone numbers at their house.)
The book Ziva is reading is not upside down. It is in Hebrew and so read the opposite way a book in English would be.
Originally aired as a 2 hour episode. Subsequent airings broke it down to 2 parts.
Abby, Ducky and Palmer are upstairs in the episode's first scene in the bullpen due to a random bug sweep. Each acts out characteristics of the owner of the respective desks they were occupying, much to McGee's consternation.
The same diner where Jenny was killed was later on used in Day in the Hole (2022) for a bar fight where Officer John Nolan and Officer Gabrielle Navar break up a bar fight.