There are several instances of J.J. Abrams' red fetish in the episode - Syd's red dress, red truck, red sweater, red hair, the red flash of the secure agency room, etc.
Greg Grunberg appears as CIA agent Eric Weiss. Throughout all of the first season of Alias, for unknown reasons, Grunberg is uncredited for his work on the show.
When Vaughn meets Sydney in this episode, it is the day when his father's watch stops working.
Marshall is the first person to reference "47."