Two of the characters from Men in Black (1997), Agent K & Agent J, are mentioned by Castle. In the movie Men in Black³ (2012), the actor who plays the young Agent K is Josh Brolin who is the real life son of James Brolin who plays Jackson Hunt (Castle's father) in this show.
Though they didn't share any scenes together, Stana Katic and Carlos Bernard both appeared in season five of 24 (2001); Bernard was part of the main cast, and Katic had a guest starring role in three episodes.
Castle mentions that Warburg sounds like a Bond villain. Stana Katic was in the Bond movie Quantum of Solace (2008).
The information Warberg give to Beckett and Castle regarding a drone pilot seeing the rose petals in a car and aborting the mission to strike is real. The US Army did in fact encountered that situation when deploying in Afghanistan, where a targeted vehicle belonged, in fact, to a couple of newlyweds instead of terrorists. The information leaked, giving military commanders further arguments to leave the ultimate decision to strike to a human pilot.