The entire episode is an homage to "Lone Wolf and Cub", a Japanese Manga about a disgraced Shogun who becomes a wandering Assassin who travels with his infant son as they seek revenge on their betrayers.
The quote "Only the paranoid survive," was from former Intel CEO Andy Groves and is also the title of his book.
Darren and Reese discuss the Art of War by Sun Tzu, a 5th-century BC Chinese general and strategist. It is considered one of the seminal studies of military tactics and strategy, influencing western military procedures into contemporary times. First translated into English in 1905, it has been translated multiple times and studied widely by both military and non-military strategists.
Amongst the items in Darren's room is a poster for the anime Samurai 7 (2004), an adaptation of Akira Kurosawa's Seven Samurai (1954) which Reese is seen watching in Pilot (2011).
Ferdy's Bar is a direct reference to the movie Memento, which was based on a short story by creator Jonathan Nolan and directed by his brother, Christopher.