Oh and there was an episode earlier this season that seems to be a definite Firefly-like reference. From Wikipedia:
"87 6 "The Final Frontier" Jonathan Frakes Kate Sargeant November 5, 2012 10.02
One of the fans of a cult science fiction television show is murdered at a fan convention, leaving Beckett and Castle caught between avid fans and celebrity egos. Suspicion turns on the cast of the original show when they learn that the victim was resisting plans to revive the series for modern audiences. This episode contains multiple references to Nathan Fillion's leading role in Firefly (referred to as "that Joss Whedon show"), a short-lived science fiction television show, that actually has reached cult status. "
Agreed! The Mal moment is brilliant but I love that they're not afraid to bring it up again as well (kind of like Big Bang Theory referencing it every so often... there are a lot of people out there still slightly bitter about that cancellation)