The closing card reads "In Memorium: Fred Chalfy, Anthony Monteforte". Fred Chalfy was a property master and set dresser who had been with the show since the beginning. Anthony Monteforte was with craft services.
The episode's title probably refers to the person called "Deep Throat," who supplied information to reporters Bob Woodward and Carl Bernstein about the Watergate scandal.
This episode also appears to be inspired, in part, by the unsolved murders of two women in Houston, TX. These murders occurred three days apart. Both victims happened to be named Mary Morris, and were of no relation. The first Mary Morris was found murdered on October 12, 2000. The second was found on October 15th, in nearly the exact same spot as the first Mary. Both of them were found dead in their burnt cars. In this episode, a homicide victim happens to be driving the exact same make, model, and color of car as a lady who was actually the intended target. In the Mary Morris homicides, theories suggest that the first Mary Morris was murdered by mistake, that the killer meant to kill the second Mary, and then corrected his mistake three days later.
This episode appears to be based on the vote recount in the 2000 United States presidential election.