They like to slip very subtle Firefly references into Castle. The first one I noticed (and I wasn't even sure if it was a reference at the time) was one where he shot a bad guy in the knee, Beckett tells him, "Nice shot!" and he says, "I was aiming for his head."
More recently, Beckett and Castle corner some Asian bad guys and Castle surprises Beckett by speaking to them in Chinese. She asks him where he learned it, and he says, "TV show I used to love."
Also the Halloween episode from a few years back, where he dressed as a Space Cowboy and his daughter asked if he was over it yet...