Ari's SUV's distinctive-font license plate - 724 TJA - was also on the car rented by the two navy pilots who were killed at the start of Twilight (2005).
Ducky tells Gerald he came to the meeting with Ari so he wouldn't shoot Gerald's good shoulder 'otherwise you might never come back to work.' Coincidentally, Gerald never did return.
At around the 30:00 mark, when McGee is standing in front of the autopsy drawer, you can see Tony's reflection in the metal doors behind him.
Ducky's cell phone ringtone is "Scotland the Brave", often considered the "unofficial" Scottish National Anthem.
Following Dr. Mallard's instructions to drive off in his car, Gerald mistakenly gets in the left side, forgetting that Ducky's vintage Morgan is British, with the steering wheel on the right.