A number of people have reported that alternate history, sci-fi romp Iron Sky contains a reference to Wing Commander. This exchange between two main characters happens around the 55:20 mark:
Cff points out that in the German dub, this line becomes "Ich kann ein UFO fliegen, ich habe alle Teile von “Wing Commander” durchgespielt."
Renate: Do you know how to drive this thing?
James: Well, it can't be any different than playing Wing Commander.