When Castle first hears that the crime scene is the Nebula-9 ship, he starts bashing the show and says "I'm a fan of good sci-fi. Star Trek, Battlestar, that Joss Whedon show!" 'That Joss Whedon show' was Firefly where Nathan Fillion played Captain Malcolm 'Mal' Reynolds.
The closing musical theme is sung by William Shatner, who played Captain Kirk in the original Star Trek series.
Castle states that Nebula 9 was not a real science fiction show because it only aired 12 episodes. Firefly (2002), starring Nathan Fillion, only had 14 hour-long episodes (including the 2-part pilot), plus one that was never even aired. Hence, 12 aired episodes.
When Castle first hears of a murder at Supernovacon, he says, "There's been a murder at Supernovacon?... Shiny!" The slang "Shiny" is used in the Firefly series, which starred Nathan Fillion, to mean "cool".
Jonathan Frakes: The fan who received Castle's autograph, better known as Commander William T. Riker of Star Trek: The Next Generation (1987). He calls himself Castle's "number one fan" and on ST:TNG, Frakes was often called "Number One."