Death and the Maiden is a motif in Renaissance art, starting from the painting Death and the Maiden (Der Tod und das Mädchen) by Hans Baldung Grien (1517). The title has since been used in, among other things, music, film (Roman Polanski) and literature.
Damon makes a reference to the 2000 Tom Hanks movie Cast Away when he compares Amara's sanity to guys stranded on islands talking to volleyballs
The triquetra formed by the doppelganger blood was the logo of Charmed (1998), which also aired on The CW (or for the most part its predecessor The WB) a few years earlier.