In the opening scene Topher says, "She went totally cylon on me." A reference to Battlestar Galactica.
Echo refers to her mind as the House of Ideas. This is a popular nickname for Marvel Comics, as well as the name of an actual location within the fictional Marvel Universe. Joss Whedon has had a lot of involvement with Marvel, both in comics and in movies.
Final appearance of Matthew Harding, played by Keith carridine