During the scene where McGee puts up the HMS Sparrow-Hawk's ship manifest, weaponry from the Halo game series is listed under armaments including 1x Magnetic Accelerator Cannon(MAC), 3x Shiva-Class Nuclear Missiles, 40x Archer missile pods, and 8x 50mm Point Defense Guns. This scene is also unusual because the HMS Sparrow-Hawk is a transport vessel which do not commonly have ship-borne weapons.
The Royals Marine's name, Pete Malloy, is identical (including the spelling) to the Martin Milner character co-starring in the 1968-75 cop TV series Adam-12. It is a Donald P. Bellisario signature to use common/familiar names for his characters, but also, Mark Harmon (Gibbs) guest-starred in an episode of Adam-12. (This is slyly referenced in another NCIS episode where Gibbs is forming an undercover identity. "Call me anything but Gus," he says. In the Adam-12 episode, Harmon played a cocky, egotistical rookie named Gus.)
The money launderers last name is Dufrane this may be a reference to Shawshank Redemption.