The sign on the wall in the Bethesda computer lab recites an old mathematics joke: "There are 10 types of people in the world; those that understand BINARY and those that do not". "10" is the binary representation for the number "2".
When Gibbs asks Karen Wilkerson for a smoke, she pulls out a pack of fictional Llama cigarettes, bearing a logo closely imitating the logo for Camel cigarettes.Abby also tested these against the fictional Triboro cigarettes, that bear a resemblance to Marlboro cigarettes that are in a blue pack instead of red.
On the screen displaying the USPS records for Dion Lambert, it indicates that his alias is Chad Murray - that is the name of Sean Murray's brother, who also was an associate producer for many episodes. (It is not clear why Lambert's alias would be part of USPS records.)
In Doppelgänger (2005), as Gibbs is walking Mrs. Wilkerson from the meeting to which she was late, they pass a painting of a ship to their left, a "Man of War". The same painting is used in The Artful Dodger (2015) in which a bug is planted in the painting.
Sasha Alexander and John Doman also star together in Rizzoli & Isles (2010), she plays his daughter.