I have begun watching Castle (in rerun) and have a chuckle every time there is a Firefly reference made. Nathan Fillion always gives a little smirk/wink.
Season 4, episode 16 - Setup: Martha asks Castle if he has heard about "Serenity" (a spa in the catskills)
Season 2 episode 6 - Vampire Weekend: Castle puts on his Halloween "costume", a space cowboy, the same he wore in Firefly ("like 5 years ago", as Alexis says - the entire dialog is hilarious).
What (if any) are some other episodes (season and number) with references to Firefly?