In their meeting, Sheppard quietly asks, "Did I have a goatee?". This is an homage to Star Trek (1966)'s Mirror, Mirror (1967), where Kirk, McCoy, Scotty and Uhura find themselves aboard a parallel Enterprise in a mirror universe, in which Spock is sporting a goatee. Going back further, this can be an homage to many "B Sci-fi movies" of the 1950's--specifically, Forbidden Planet (1956).
Before the opening credits, McKay asks the group if they know how many addresses are in the Atlantis database that have no accompanying description. Sheppard replies "42." This is a reference to "The Hitchhiker's Guide to the Galaxy".