Chuck asks Casey if it's possible that someone kidnapped Sarah and replaced her with "some kind of soulless replica." The actress playing the agent who replaces Sarah is Tricia Helfer, best known for her role as the Cylon "Number Six" in the TV series Battlestar Galactica (2004).
The date of birth used on the fake Canadian passport of Agent Alex Forrest (shown during one of Chuck's flash sequences) is April 11, 1974, which is the actual date of birth of Tricia Helfer, the Canadian actress portraying the character.
The alias, Harry Lime, is a nod to the classic book and film, The Third Man (1949). Harry Lime is the main antagonist of the 1949 film, and was portrayed by Orson Welles.
When Chuck enters the hospital room of Rashad Ahmad, Dr. Zamir (played by Shaun Toub) greets him with "Doctor". This sets off a comical back and forth of "Doctor, Doctor, Doctor, Doctor, aaaand Doctor", a classic reference to Spies Like Us (1985) when Millbarge (Dan Aykroyd) and Fitz-Hume (Chevy Chase) meet the other Doctors Without Borders physicians that they are embedded with.
When Sarah is searching names on the Castle's computer, one of the ones that flashes on the screen is Robert McNeill. Robert Duncan McNeill is the supervising producer on the episode.