Based on a simulation used by the CIA according to Faisal the man who knows nothing.
At the Post office you can find a pair of Sam Fisher's trifocal goggles from Tom Clancy's Splinter Cell Franchise
In an "Echo" (01 General, End of the World Party) found in Clinton, you can find two men standing off to the side named Jonathan Pinkman and William White, a nod to Breaking Bad. In the description for White it shows: "Occupation: Chemistry teacher" and "Details: Operated a car wash". For Pinkman: "Occupation: Unemployed" "Details: Criminal record".
In the mission "Rooftop Comm Relay" your assignment is to protect a JTF technician called John Reese. His name derives from John Connor and Kyle Reese from the "Terminator" series that also deals with the fall of society, though in a more apocalyptic way. Another possibility for this easter egg is that the name is a reference to the main character of the hit CBS show Person of Interest by the name of John Reese (Jim Caviezel), who works to protect New York City from organized crime with the help of a super artificial intelligence.
In an "Echo" (#26, Shortcut) found in the northern portion of Chelsea there is a reference to the movie Shaun of The Dead. The man identified in the "Echo" is named Shaun and he speaks the line: "What, never heard of a shortcut before?" then is heard falling through a fence he is supposed to jump over, just like in the movie.