LORELAI: You have crossed over into the dark side, Luke.
An obvious joking reference to the Star Wars science-fiction movie franchise, which has Luke Skywalker (Mark Hamill) as one its major protagonists, and “the dark side” as the forces of evil. More specifically, it is a reference to the 1983 Return of the Jedi; in the movie’s final fight scene, Luke is tempted by the Emperor to kill his father and cross over to the dark side.
Return of the Jedi was the #1 film of 1983, and received mostly positive reviews. It won a Special Achievement Award for Visual Effects at the Academy Awards.
Fans of the films may find Lorelai’s comment amusing (or thought-provoking) in light of the more recent films in the franchise.