Tony uses the alias "Stringfellow Hawke" at one point; also, Caitlin Todd's first name is the same as an Airwolf character.
In one episode the team finds a massive collection of lunchboxes in a murdered officer's bedroom, which included Airwolf, and Magnum, P.I.-themed boxes, and presumably other Bellisario creations. And when Tony must provide an alibi for his evening, he says he was home watching Magnum PI, and describes the specific episode.
Yet another crops up when searching a suspect's house in one episode, and Tony finds, among a full collection of Hawaiian shirts, a red one he claims to be an official Magnum PI shirt.
"Hiatus part 1" has Tony at one point say, "I have a better chance of hooking up with Jessica Alba than these guys do of infiltrating Sealift." Michael Weatherly, the actor who plays Tony, costarred with Jessica Alba in Dark Angel, and was engaged to her.
Gibbs shares a middle name (Jethro) with Admiral Chegwidden from NCIS' parent series, JAG.
In the second episode (not counting the JAG-crossover Pilot), Gibbs talks to Lieutenant Bud Roberts from JAG, though some may claim this to be more of a Continuity Nod.
And retired Admiral Chegwidden appears in the season ten finale as an attorney hired by Director Vance to represent Gibbs.
One episode's supporting characters are a huge Shout-Out to G.I. Joe. There's FBI agent Courtney Krieger (Cover Girl), as well as Carl Greer (Doc), Shannon O'Hara (Scarlett), Marvin Hinton (Roadblock) alias Frederick LeClair (Recondo), Robert Graves (Grunt), George Barny (Grand Slam), and Blaine Parker (Mainframe).
Amusingly, in one episode, McGee stepped into the victim's computer hideout and exclaimed "this is like the TARDIS!"
Actually, far too many to list, as Tony is almost guaranteed to make at least one TV or movie reference every episode.
Normally, the team is not familiar with most of Tony's movie references. However, when he loops a video feed to save a room of hostages, everyone calls him out afterwards when he tries to take credit, knowing which movie he stole the tactic from.
Arguably, the joke here is that Tony had forgotten the film-inspired origins of his idea and is actually convinced he thought it up himself. Look at his expression! (Unless Anthony DiNozzo is a better actor than, say, Michael Weatherly...) Of course, none of the rest of the team believe him for a moment.
In the second episode of season 4 "Escaped" Ziva and McGee go to extreme lengths to avoid the word "fugitive" to keep Tony from connecting the situation to The Fugitive. Tony eventually comes to the connection on his own and monologues his own foolishness while Ziva and McGee whisper to the side:
Ziva:What happened? We have been avoiding mentioning the Fugitive for days McGee:He figured it out for himself.
In the very early episodes, Gibbs is the one who is movie savvy.
In the ninth season episode "Enemy on the Hill", the name "George Kaplan" emerges during a murder case involving money laundering, prompting Tony to comment, "That sounds familiar." Later, when "George Kaplan" turns out to be an alias used by the real killer, Tony says, "I must be slipping" when he remembers the name as the non-existent CIA agent from Alfred Hitchcock's North by Northwest.
It could just be my imagination but the background music for "Better Angels" sounds a lot like "The ForceTheme". It might have something to do with the good man from an evil empire who needs to know he's still a good man despite what he did during the war. Also based on a true story.
One episode has Tony referencing Aliens, complete with imitating the movie's namesakes signature scream. Cut to Ducky dissecting a small animal under a magnifying glass in a shot almost mirroring Bishop dissecting the facehugger in Aliens.
Kate: Gibbs, what did Ducky look like when he was younger?
Elle's obsession with capturing the terrorist Parsa is an obvious shout-out to Agent Maya's obsession with Osama bin Laden in Zero Dark Thirty, though unlike the film/real life Elle isn't a Fiery Redhead, she's met Parsa in person and has some kind of "personal" relationship with him (one of them even knows what the others favorite health bar is), Parsa is captured alive but gets shot by Elle after he attacks her.
"Obsession" is almost a Whole Plot Reference to Laura, but since the title refers to Tony, it falls to Ziva to point out the parallel.