Gibbs' right eyebrow and surround clearly shows the damage received in the previous episode.
USS Rubicon was played by the former USS Paul F Foster (DD 964), the second Spruance class destroyer. It was decommissioned March 14, 2003 in its home port of Everett, WA and is now serving as the Navy's Self Defense Test Ship in Port Hueneme, CA.
The ship that is being salvaged in Road Kill is really the USS Paul F Foster, which is the same ship Gibbs, Tony and Kate supposedly board looking for a murderer in The Immortals (2003).
When Ducky is about to start the autopsy, he says that, according to legend, Aeschylus died because a vulture mistook his bald head for his prey and dropped a stone on it. This is partially true: a bearded eagle dropped a tortoise on Aeschylus head having mistook it for a stone suitable for shattering the shell of his prey
When McGee is searching Kapp's license plate, he enters Virginia license 724 TJA. This is the same plate that was on Ari Ashwari's SUV in the episode Kill Ari (S3e1)