Bud being a sci-fi nut; he gives the occasional reference to Star Trek and Quantum Leap, even naming one of his kids after James T. Kirk. Donald P. Bellisario even cameos as himself at a sci-fi convention, and his star on the Hollywood Walk of Fame is featured in one episode. The Star Trek connection is interesting considering it has the same copyright holder as JAG (i.e. CBS / Paramount.) Cross-promotion anyone?
The name of the fictional aircraft carrier USS Seahawk, first seen in the pilot, is probably an homage to that Errol Flynn movie.
It is also interesting the first Scifi reference in the show - in the pilot, when Captain Boone (the CAG) and Lieutenant Arrutti return from a flight, as Boone is about to get out of the cockpit, one of the yellow-shirt flight deck crew starts to paint on the F-14.
Captain Boone:Chief, if I bagged a Klingon, I believe you'd know what Flag to paint on her.
Chief Ned Bannon:Klingons are Easy, now a Romulan Warship now that might be a problem, they're invisible.
So there's Trek fans among the fictional Seahawk crew aside from Bud, so an implied subversion of Hollywood Nerd.
In "Pilot Error", Harm compares the situation to the movie Fate is the Hunter, explaining to Meg (who hasn't seen it) how they found out the cause of a plane crash by recreating all of the minute details of the flight.
Lieutenant JG Meg Austin: John Wayne was being chased by Iraqis?
Lieuteant Harmon Rabb: Indians!
Corporal John Edner: Right in the middle of Monument Valley.
Lieutenant JG Meg Austin: Bet they didn't have a woman with them.
Lieuteant Harmon Rabb: You'd bet wrong! They had a woman a lot like you: Claire Trevor.
Corporal John Edner: Yep, prostitute Duke fell for.
Lieutenant JG Meg Austin: You're comparing me to a prostitute?
Corporal John Edner: No, ma'am. I didn't say that.
Lieuteant Harmon Rabb: I did, and I meant she was spunky like you.
In "Boot", an episode centering on an investigation into the death of a Marine recruit at Boot Camp, the two Drill Sergeant Nasties spend some idle time watching The D.I., an old Jack Webb film about Marine Boot Camp. This also serves as some clever foreshadowing if you're familiar with the film's history, being made in response to a highly-publicized incident where several Marine recruits drowned while marching through a swamp at night. The film's climax has the killer and Meg Austin both nearly drown in the swamp during a nighttime foot chase.
In Season 2’s "Washington Holiday" (itself a take on Roman Holiday) when the Romanian Princess has escaped from doing her duties and went to a night club instead: Harm, as her military escort dressed in whites, carries her back to the limousine causing a woman in the background to say: "This is so like An Officer and a Gentleman".
In "The Game of Go", when Harm, Mac & Bud meets Clayton Webb at the U.S. Embassy in Bogota.
Bud Roberts: Well, there were actually four musketeers, sir. Athos, Porthos, Aramis and D'Artagnan.
Mac questions an enlisted marine about their captain’s unorthodox training methods in "Force Recon". Considering that the captain has the nickname Duke like John Wayne, she comments that there seems to be case for movies.
Sergeant Tesla: Captain Koonan is the finest officer I've ever served under, ma'am. I'd follow him to hell and back.
Josh Pendry: Steven Seagal in Under Siege. He got the Pentagon on a satellite radio from a life boat.
Lieutenant Commander Harmon Rabb: Well, unfortunately this isn't a movie, Josh. These lifeboats have satellite radios with an emergency beacon and a short-range voice transmitter. We could activate one. The Coast Guard would come, but before we could inform them of our situation, who knows what these terrorists are likely to do.
Big Bud: "Speaking of Harm, how you're doing Perry Mason!"
In season 5, episode "Rogue" centers on a Navy commando who has recruited Navy SEALS, Delta Force and other assorted Bad Ass soldiers to infiltrate and attack military installations, including nuclear submarines, to test their security and advise on how to defend against a terrorist attack. Despite claims that it's not based on real life the episode name hints at the fictional and real life exploits of one Richard Marcinko.
"The Colonel's Wife"
Mac (to Harm): Interesting investgative technique, Sherlock. Why follow a subject when you can have them give you a ride and a kiss good night?
In this episode we learn that Bud's favorite movie character is HAL from 2001.
Bud (imitating HAL): As a computer, I find you faith in technology amusing.
Bud's former college roommate Ron Katz asks Harriet:
Bud bonds with a suspected terrorist by discussing the merits of the Prime Directive, as both are fans of Star Trek, using this to obtain useful information. (All this as opposed to an ineffective asshole CIA Officer who’d advocated torture to extract information.)
When in Afghanistan with Harm, Mac starts to talk about that classic western.
The Hunt for Red October is even namechecked when Sturgis compares himself and the Russian renegade sub captain being chased to Alec Baldwin and Sean Connery respectively.
Commander Turner: With your permissions admirals, I'd like to volunteer for TAD aboard the Watertown. Vice Admiral Holt: Commander, as much as I respect your service as a submariner, Commander Flagler is perfectly capable. Commander Turner: ''And I don't mean to imply that he isn't, sir, only that I am Alec Baldwin.