Zach argues with Lane's uncle Joe, played by Chase Kim, by saying "Welcome to the S.H., bitch." This is a reference to The O.C. (2003), which stars Adam Brody, who played Lane's previous boyfriend, Dave. Chase was also in an episode of the O.C. in 2006.
Rory cites Gwen and Gavin as an example of a couple that made it through a tough time, and said she thinks they are still together. For the record, they were still together when this episode was made in 2006, but they eventually divorced in 2015.
When Rory brings flowers into their apartment, Paris says "Bring 'em on in, Algernon."
This is a reference to the classic science-fiction story "Flowers for Algernon", by Daniel Keyes.