Early in the show, Binghamton refers to a news article written about a 'hot-roger' of PT-109 that made him full Lieutenant. He is referring to John F. Kennedy, President of the US at the time of airing. PT-109 was an 80' Elco Patrol Torpedo boat last commanded by Lieutenant John F. Kennedy, future United States president, in the Solomon Islands campaign of the Pacific theater during World War II. This episode aired only 18 days before Kennedy's assassination.
The title is derived from the Jolly Roger, a name given to any flag flown to identify a pirate ship's crew and the most common design is the skull and crossbones on a black field with the long ones in an "x" configuration.
On this episode, the door to Binghamton's office is hinged opposite its normal arrangement (on the left side as seen from inside the office, and opening outward), in contrast to its usual hinging on the right and opening inward. This was probably done to facilitate the action dictated by the script.