When Whitman hands Sophie a drink in his office, there are two awards/degrees hanging on the wall behind him. One says Bellbridge University and the other Culpepper University of Academia. Fans recognize that as the name of the city and corrupt mayor from Season Two's "Three Strikes Job" and "Maltese Falcon Job".
Eliot and Hardison use the aliases of IRS agents Brody and Quint, same names as the police chief and fisherman from the movie Jaws.
When Nate steals the train for Eliot and Hardison he mentions it's coming from a beet farm in Pennsylvania, this is likely a reference to Schrute Farms from The Office.
The part of the episode when Eliot and Hardison are handcuffed together and trying to escape the militia is the basis of the movie The Defiant Ones (1958) starring Tony Curtis and Sydney Poitier as escaped convicts chained together on the run.
At 15:03 the camera does an overview pass of a city. The building it passes over is Fountain Place located in Dallas, Texas.