These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: The Chameleon in Season 3. The guy murders a lot of people, including Agents Renko and Hunter, then tries to have the rest of the NCIS team killed to get at Callen. He also forces the American government into a Sadistic Choice with the Iranian government as a means to release him, a choice that is strongly implied to be a pointless gesture for the American government as the Chameleon's only going to reveal the secrets on American intelligence to the Iranians anyway. His faked death in the Season 3 finale, that results in Callen's arrest and a breaking news story, was very well deserved. Hetty sums him up best:
Hetty: He [the Chameleon] is many things, Granger. But he is one thing that he is not and should be... dead.
"Sam sees the glass as half-full. I see the glass as half-empty, that's why we make such a good team. Kensi, on the other hand, drinks straight out of the bottle, Nate wonders why it's a glass and Eric usually breaks the glass by putting his feet on the table."
After Eric explains how he stopped the release of a terrorist's threat video
Hetty: In English, Mr. Beale.
Eric: Oh. I broke the Internet.
Deeks on the shooting range.
Protagonist-Centered Morality: At times, when the team is on affairs beyond their jurisdiction. Most egregious example is when they went to Eastern Europe and massacred people, criminals or no.
Foe Yay: Hetty pretended to be Kohl's wife for so long she acknowleges it's the closest she's ever been to actually being married.
Germans Love David Hasselhoff: In Portugal, most promotional materials and ads for the show focus near exclusively on Kensi (played by Portuguese actress Daniela Ruah) to the extent that you'd think she was the main character.
Harsher in Hindsight: Sam suggests that the potential black ops mission to rescue ex-Marines in Dubai in the episode "Recruit" can be blamed on Mossad.
Hilarious in Hindsight: Everyone's mockery of the idea of Nate in the field. Considering how awesome he is in the field now ...
Hanna: I really look forward to having Dom as a partner. Callen: You'd miss me. I complete you.
This immediately after Callen asking Hanna if he had a history with their suspect, and Hanna responding with "We weren't dating, if that's what you're asking."
Kensi once asked Hanna how long he and Callen had been married. At what point does it stop being subtext?
Probably one episode before that when Hetty suggests Callen take out the attractive treasury agent, and then take Sam out the next night so he "doesn't get jealous."
The hoyay between Sam and Callen has just been increasing over the past few seasons... or at least, the implications on Callen's side have, culminating in the 4th season finale, where The Chameleon singles out Sam as his target to hurt Callen with, going so far as to refer to him as Callens "beloved partner".
Iron Woobie: Hard not to see Callen as this after everything he's gone through.
"Pushback." It turns out that the Russian woman Callen was avoiding out of suspicion in the "Legend" pilot was his little sister! (well, as good as.) She was there to warn him that someone was trying to kill him. And to make it all worse, she was killed in the beginning of the episode while trying to get revenge for Callen, who she thought had died when he was shot.
"Missing." Dom is kidnapped, and the team is unable to find him and have no leads by the end of the episode. The missing person report at the end only makes it worse.
It gets worse. "Found" is pretty much the definition of Hope Spot. They know where Dom is. He gets given a key and breaks out of his chains. They meet up with him in the middle of a firefight... only for him to get fatally shot when he's trying to run to safety.
Too Soon: Averted in "Neighborhood Watch": in the wake of the Trayvon Martin shooting a movie changed its name to just The Watch and a reality series of the same name about watchmen was apparently canceled; not this episode. A lot of people get shot in a gated community in a sunny state, though none of them were black (a few wear hoodies, though).
Actually, make that Deeks full stop- he has a tendency to look so utterly broken and exhausted even when he's still going that it's almost like he's got a giant flashing neon sign around his neck that says 'I'm A Woobie'.