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 life 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.
It gets more interesting: Gibbs' daughter was around 9-10 when she was taken from Gibbs. Ziva ends up being with Gibbs for 8 years before leaving. In essence, Gibbs had a daughter for roughly 18 years and had an experience of letting his daughter leave the nest.
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.
Forget friends, Ari was Sergei's half-brother!
It also explains why Sergei's final murder in the episode "Check" echoes Kate's, which Ari committed.
In the episode "Life Before His Eyes," Gibbs spends most of the episode in a 'purgatory' diner populated by the people in his life, both living and dead. Only one currently living character says anything to Gibbs inside the diner: Ducky, because Duck talks to the dead.
He also sees his younger self embracing the female recruit he had a crush on, indicating that despite the happiness he had with his wife and daughter, a part of him might still regret never having the nerve to approach her.
In "Judgement Day", Ducky has the Right Behind Me realization after making a joke about Gibbs. It seems typical of this show and this trope, until you recall that he's sitting at Tony's desk and imitating him—and Tony is usually the one who gets snuck up on.
Speaking of which, ever notice that when anyone else takes the lead on the case—Ducky, Tony—it's they who ends up pulling this? It makes sense. They are taking over Gibbs's role, after all.
Gibbs apparently picked up his elevator trick from Mike Franks. But Pride accuses him of stealing it from him. It sounds like a continuity error, except that they were both probationary agents under Franks and no doubt both picked it up from him.
In "What Lies Above", Quinn is the only one on the team who didn't know about the triple homicide that took place 15 years ago in the apartment that Tim and Deliah (previously Tony) own before the events of the episode. That makes sense when you remember that she was the only one who wasn't competing for Tony's old apartment in "Home of the Brave", so she wouldn't have needed to know why the place was so cheap compared to it's surrounding neighbors.
There are actually some major plot holes in Tony and Jeanne's romance. She never notices that (a) She hasn't met any of his friends or family? (b) She's never been to visit him at his job? (c) She's never been to his place? In Real Life, these are warning signs that a woman is actually the "other woman" rather than a legitimate girlfriend.
Most of these can be justified. He can make up his own background story to explain away the lack of family members. Because he was undercover he may have been using a second residence as his place, which she could visit. Why would she visit him at his job? Depending on the nature of a person's work that may just be impractical, or simply boring.
In "Institutionalized", the prime suspect is Kasie's childhood friend, Dante (who has gotten in trouble with the law prior to this episode), and she keeps insisting to the other team members that he's innocent and fighting tooth-and-nail for her friend. At one point, Vance praises Kasie for her determination and loyalty and has no intention of telling her to stop; however, he asks her if Kasie is one-hundred percent sure Dante is innocent of the murder. This makes sense when you remember he went through a very similar situation back in Season 9's "The Good Son"; his brother-in-law, Michael (who has also gotten into trouble with the law prior to that episode), was the prime suspect in that week's murder, and despite Vance's insistence that he's innocent, it turns out that Michael was the killer, leaving Vance no choice but to have him be arrested. Vance sympathized with Kasie's situation, but he was also worried that it was going to end the same way. Fortunately, in Kasie's case, Dante turned out to be innocent, the real killer got busted, and Dante managed to get that interview for being a dog-trainer at the end of the episode.
In "Ephemera", the main characters imagine themselves as characters in the victim of the week's life story while they're piecing together how a rare and valuable coin wound up in his possession. Ducky is the only one who isn't imagined as any of the characters during the story. However, Ducky was the one who suggested that Team Gibbs imagine themselves as the figures described in the letters in the first place. Between that and him being the NCIS Historian, this makes him the organizer and narrator of the story.
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 similar circumstances years ago. This is probably going to bring up horrifying memories for him.
Gibbs' fondness for Ziva is explained by the fact that she's the same age that his daughter would have been had she not been killed. Now Ziva is also dead, meaning that Gibbs has essentially lost his daughter twice.
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.
More like Fridge Tearjerker, but Gibbs' fondness for children gets this when we learn what happened to his wife and daughter.
In "What Lies Above", a dead body (or what's left of it, rather) is found under the bedroom floorboards in McGee's apartment. Everyone freaks out at the realization that Tim and Delilah have been sleeping—and, you know, not sleeping—over a friggin CORPSE (and even worse, as of "Something Blue," it is possible that Delilah and Tim's twins were conceived before the body was removed). But it gets even worse when you remember that the apartment used to be Tony's. This means that for almost 15 years, he (and his, ahem, overnight guests) have been sleeping and not sleeping over that thing too. It would have been nice to know his reaction to that.
In Season 8's "Pyramid," Ziva is kidnapped by the Port-to-Port Killer, mostly as a distraction. Tony and Gibbs are livid, and both end up threatening Trent Kort with bodily harm, as he is the one who possibly sent her into a trap. They (or at least, Tony) gets called out on the excessive response, but it's not until Tony says "It's just different for some of us" that you realize it's been only about a year and a half since Somalia, and it's probably bringing back some horrible memories of the last time Ziva went missing.
There's some considerable Fridge Horror at one point in "House Divided" when one of Gibbs' and McGee's captors bangs on their cell door with a baseball bat and Gibbs jumps back fearfully. Just how many beatings has he taken from that bat that he would react like that?
In "Bears and Cubs", Jimmy reveals that his long-dead father "was not a good man at all". The freaked-out way he says this statement and his refusal to elaborate on the details really bring some horror to the imagination.
Sloane established herself as the Team Mom, always cheerful and smiley...and then it was revealed that she was captured and tortured in Afganistan. And then it's revealed that before that, she was raped. And she's still haunted by both traumas. Now the cheerful Team Mom seems more like a Stepford Smiler.
The climax of "Family First" has the team, particularly Tony, enact a Roaring Rampage of Revenge against Trent Kort for ordering the attack on the farmhouse that supposedly killed Ziva. That is explicitly the reason given as to why they all just open fire on him. Except, as revealed in season 17, Ziva is alive. Meaning the team just gunned down a man in cold blood with no concrete reason—yes, he'd killed other agents, but that's a reason to arrest him not kill him. This is never addressed.
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.
A person whose allergies are that severe would know exactly where her Epi-Pen is at all times. But they might fail to share their allergy or where they keep their epi-pen with their travel companions.
In "What Lies Above", a dead body (or what's left of it, rather) is found under the bedroom floorboards in McGee's apartment, which used to be Tony's. How the hell was no one aware of this? Decomposing bodies stink. Even the rotting carcass of something as small as a rat can stink up an entire house. You can only imagine how bad a full-grown human body would be. There's no way that someone else in the building wouldn't have noticed or complained. And even if all decomposition was done by the time Tony moved in, there probably would have always been a lingering odor that he would have always complained about.
Except that the person who hid the body was adapt prepping skins and bodies for long term storage. He was caught with bodies he didn't have time to prep, unlike the one in the floor in which he had days or at least a few weeks to prep for storage in the floor making sure it wouldn't smell or possibly even decompose.
The pilot episode, "Yankee White", makes a big deal of the Jurisdiction Friction between the FBI, Secret Service, and NCIS during the investigation of a naval officer's death aboard Air Force One. It's mildly puzzling that Air Force OSI didn't manage to get in on it as well, since there would be an AFOSI detachment at McConnell Air Force Base, located in Wichita, Kansas (compare to NCIS, which had to take two flights from the East Coast to get there). On that note, it's never really explained why Air Force One put down at a civilian airport in Wichita, rather than at the Air Force Base, where the plane (and the President) could be better secured and protected.