During the police interrogation of Lee Tong, Castle attempts to prove that he's a ninja by knocking over a cup of coffee, referencing a scene in "Revenge of the Ninja" where Cho Osaki catches it before it hits the ground and without spilling a drop. When Lee Tong fails, spills coffee everywhere, ands breaks the cup, Castle states that he's not a ninja.
When the Japanese consulate dismisses Castle's ninja theory, he says to Beckett, "What does she know anyway? I bet she's never even seen Ninja III: The Domination".