In "Chimera," Commander William Skinner, who is in charge of the titular "black ship," is played by Steven Culp. He also played Clayton Webb, a CIA agent who had faked his own death in the parent show of JAG. Think about that for a second.
In "Toxic", Palmer picks up and expands on Ducky's explanation on the reasons one would or would not wear shoes historically and explains that he once wrote a paper on- he gets cut off before he can name the topic, but it's obviously something to do with shoes. Why would Palmer write such a paper? Because he has a shoe fetish.
When asked by team members what Ducky looked like when he was younger, Gibbs replies "Illya Kuryakin". Illya was - of course - played by David McCallum: Ducky himself!
You know how, in NCIS, Tony keeps making pop culture references, while Ziva can hardly get any idiom right? Notice how Tony's always talking about his sex while Ziva rarely does? Notice how Tony's quotes cause people to underestimate him, while it's implied Ziva misquotes on purpose to produce the same effect? Notice how they mirror each other in a few other ways? — Tropers.Jonn
The ME's name is Donald Mallard. A mallard, as his nickname (Ducky) implies, is a duck. Essentially, we have a character named "Donald Duck" on the show. — Tsunoba
That is in his backstory as how he got the nickname: he was a fan of Donald Duck and his name worked perfectly for it, so other kids took to calling him that.
At first glance, McGee appears to be the Unfavorite (at least compared to Abby, Tony and Ziva) where Gibbs is concerned. But after a few seasons of watching Gibbs interact with various people, it's clear that he cares about McGee as much as any member of his team. But while Tony, Ziva and Abby are allowed to operate with a freer hand (in part because of their respective experience levels and individual personalities), McGee is kept on a shorter leash because he HAS to be. He has a tendency to get lost in the details, become easily distracted by issues in his private life (women, his writing, video games) and occasionally is still intimidated by power (a disadvantage when investigating crimes occasionally involving high-ranking officials). But thanks in part to Gibbs and his "tough love", he's now a more proficient agent and seems far more comfortable in his own skin. And thus, a much more effective member of the team. Now, if Gibbs ever does join Mike Franks in Mexico (or wherever), he can be completely confident that NCIS (and NCIS) is in good hands. And one also gets the feeling that he's training Palmer in the exact same manner. — TVsTim1
In the pilot episode "Yankee White" it is not really strange Gibbs knew the plot of Air Force One and about the traitor. The traitor was also named Gibbs. Because of the same name and NCIS!Gibbs' patriotism he remembered the plot out of dislike of his name being the name of a traitor.
In "Faking It", an early season 4 episode, the team's prime suspect and murderer of the week is connected to an arms dealer the CIA is using named Arkady Kobach, who is killed by Mike Franks. A few episodes later, the team learns that La Grenouille is being handled by the CIA, and at the start of season 5, it's suggested that he is actually a CIA asset. Maybe after [[Kobach died]], they brought La Grenouille to take his place, and spite NCIS.
The father-daughter dynamic between Gibbs and Ziva gets a boost if one noticed Ziva's birthday when it was revealed: if you figure out how old his daughter was when she was killed by the drug cartel, it works out that she and Ziva were born around the same time. Ziva is literally his daughter's age.
At the end of season 12 premiere "Twenty Klicks", Vance mentions to Gibbs that Sergei survived Gibbs shooting him. Gibbs thinks it's impossible, but it's very possible. How? Sergei was one of Ari's friends, and took a page from "Bete Noire" - a bulletproof vest that took Gibbs's rounds.
In Life Before His Eyes, the various characters try to convince Gibbs not to let himself be killed by a random guy by showing him AUs of things being differently, because "everything happens for a reason". Only that had Kate not been killed, it would have actually been better for everyone (except Ziva perhaps), and worst of all, if Gibbs had died as a marine, Shannon and Kelly would still be alive, Abby wouldn't have had to carry his secret (or alternatively, she wouldn't have had to dealt with non-functional!alcoholic Gibbs), and everybody would be, indeed, better off.
Also, the guy who talks to Gibbs about him shooting Hernandez: Gibbs doesn't feel remorse about having killed him (and with good reason), but then he feels guilty when he's reminded by that guy that Abby knows about it and has to keep the secret now, only then Gibbs says it may have done more harm than good. Nevermind that he left, at the time, two children without a father (because Paloma and Alejandro were children back then, or that it caused them to take revenge on him and almost kill his father, or all the effects it has had on the rest of the team. Since every character and interaction was a fabrication of Gibbs' mind at the moment, one can't help but think Gibbs only thinks murdering a man could be somewhat bad because Abby (a person he didn't know back then) knows what he did. Good to know his priorities.
If Gibbs felt guilty over every single bad guy he killed who left a family behind, he probably wouldn't be able to function. That it negatively affected someone he eventually became almost like a father to later, well, that makes it personal.
Equally worrisome would be the idea that GIBBS believes everyone in his life would be better off without him.
A blink and you'll miss it moment in "Shabbat Shalom". Jackie mentions early on that the kids were spending the night at a friend's and she and Leon would have the house all to themselves for the evening. Then Eli David comes over for dinner and the house gets shot up and both Eli and Jackie are killed. What if the kids had been home?
In Berlin, it's assumed Tony and Ziva were purposely run into. Gibbs' wife and daughter died in a similar circumstances years ago. This is probably going to bring up horrifying memories for him.
In season 11 premiere "Whiskey Tango Foxtrot", what if Parsons had not tried to question Morrow about Gibbs's JSOC mission? Then, Morrow would have been killed along with Sec Nav Jarvis. Morrow owes Parsons his life.
In the season 7 episode "Jetlag", Tony and Ziva are protecting a witness on a flight to the US from Paris. One of the ways the bad guys try to kill her is by aggravating a fatal allergy to peanuts via a pillow lined with peanut dust. She starts having an allergic reaction and they are forced to use another passenger's Epi-pen to counteract it. If she had such a severe allergy, wouldn't she be carrying her own Epi-pen?
The assassin could have filched it. Also, sometimes it's faster to get something from someone else rather than take the time to look for it yourself, especially if you had no idea where exactly the object is.