When Castle is considering names for bar he's considering opening, Martha suggests "Rick's Cafe Americain" which is the name of the cafe in Casablanca. Castle also mentions that he was considering the name "Castle-blanca" which is a pun of the name "Casablanca".
At the auctionhouse, Steven Heisler asks Castle & Beckett if they know Jimmie Walker. Castle says yes but Heisler say's he's not refering to the actor who played "J.J" on Good Times.
When analyzing the dead body, Lanie says it was no boating accident. Castle then says "Then, we better close the beaches". Beckett and Lanie look at him dumbfounded. He then name drops Chief Brody & Hooper but both still have no idea what he's talking about.
When Castle and Beckett are first exploring the old abandoned underground sewers, Kate is commenting on the condition of their setting... Castle then says "Don't forget about the CHUD's... Cannibalistic, Humanoid, Underground, Dwellers." This is a direct reference to the 1984 movie, C.H.U.D.