When Tony is burning the note at the fireplace, the lovely song playing is "All We Are" by Matt Nathanson.
Tony finds a clue to the missing car, consisting of a "Dead Head" decal from The Grateful Dead. In 1988's "The Presidio" Mark Harmon's character sees a "Dead Head" poster in the office of the water delivery company and uses it to establish a rapport with the company receptionist to get the address for a suspect.
When Ziva confronts Tony about his feelings for Jeanne, Tony fights back by mentioning Lt. Roy Sanders as "the dead man walking." The episode where Ziva falls for Roy, a victim of radiation poisoning who later died, is called "Dead Man Walking."
The stuffed elephant on the dresser is Babar King of the Elephants