- Possibly Pierce and Brosnan, traitors for hire.
- In episode 4 of the first season, Search and Destroy, Sam references Spock's line in Star Trek VI about logic being "the beginning of wisdom, not the end".
- Popeye was referred to in "Free Ride".
- To the novel and soon movie Lone Survivor, with the episode in the 2/26/13 episode "Lokhay".
- Steve McQueen and Marvel Comic references abound in "Parley".
- When Kensi has to make her way out of a laser maze, she briefly recreates a slightly more tasteful version of the famous shot of Gin's rear from Entrapment. Deeks politely looks away.
- In "Spiral", Deeks calls one of the masked terrorists "Bane" due to his muscular figure and hockey mask.
- In "Three Hearts", Deeks describes their teamwork as "very TMNT" and says "Callen and Sam are totes Leonardo and Raphael".
- At the start of "Blame it on Rio", Deeks wear the yellow martial arts jumpsuit used by Bruce Lee in The Game of Death, which promptly makes everyone tease him for cross-dressing as the Bride from Kill Bill.
- There's a ton of pop culture references, probably because DiNozzo is paying a visit: he makes a twofer reference to the Lost Boys (fantasy and horror versions) and refers to the Los Angeles team as the West Coast Avengers — which is kind of odd for someone who disdains the "geekier" side of pop culture that his partner Mcgee prefers to the point where he had no idea who or what a dog called "Lockie" was named after. Rio mentions Knight Rider (he wants Magic Plastic Surgery to look like David Hasselhoff) and The A-Team while one of his many aliases is Hiroshi Sato (or Saito).
- There's also lengthy conversations about Renaissance Fairs, the Society for Creative Anachronism, and the Furry Fandom.
- When discussing cosplay with Nell, Eric mentions Sailor Moon, Lilith, Chun-Li, and even throws in a Persona reference.
- "The Prince" has the criminal group Syndicate compared to the one from the Mission Impossible films.
- In "Descent", Deeks is tortured by having his teeth drilled. It's very much like the imfamous scene from Marathon Man, complete with the torturer asking him, "Is it safe?"
Shout Out / NCIS: Los Angeles