The number on Chuck's prisoner uniform (092980) is actually the birth date of Zachary Levi - September 29, 1980.
Matthew Willig's character Yuri's code name 'Hydra' is a reference to a movie of the same name he acted in (Hydra (2009)).
When Chuck goes undercover in the prison, "Scofield, Burrows and Abruzzi" were called over loudspeakers. All of them are characters from Prison Break (2005).
Sarah wears the classic female spy black leather catsuit, which was first developed in 1965 for the character Emma Peel in the BBC spy show The Avengers (1961). That show also gave us TV's first black corset/panties, choke collar, stiletto heel boots dominatrix outfit (actually designed by Dianna Riggs, who played Mrs. Peel).
Ellie picks Grunka as a name for her daughter. Big Mike says it reminds him of Grunka Kasabian, "that famous Armenian serial killer", a reference to Linda Kasabian of the Manson Family.