Anything involving Hetty and Callen. Despite being protective of all her agents. Callen is the most like a son to her and she went out of her way to look out for him.
In "The Third Choir", Callen shows how much she cares for her by putting his life savings as a bounty on Matthias, the man threatening her life.
All but cemented in "Rage", showing that when they first met, Callen asked if he was going back to Child Services. Hetty said no, stating he could stay with her as long as he wanted. Noting he had great potential and she had a plan for him.
Hetty becoming Deeks' emergency contact.
It's a very small moment, but in "Kill House", Nell has been kidnapped by a team that professionally trains tactical units to go on missions. One of their biggest issues when they ran simulations was that they fell out of team mode, when they became deceived about their mission status. Not only has the team been curb stomped by them twice, they have a person inside. After they take care of the perimeter guards, they are all gathered together in a diagonal line but covering different directions and sight lines with their guns. When the perimeter's clear, Callan taps Deeks on the shoulder, Deeks taps Sam, Sam taps Kensi, and they all move at the same time into the building. The transition from how they ran the practice ops (very good) vs. going in for Nell (freaking surgical) was amazing and all shown in that move.
Blye, K is filled with 'em. Notably, Kensi is breaking down in the bathroom, and she calls Deeks. One interpretation is that she just wanted to hear his voice. This after she calls him the "only one she can trust" (because, screw you, Callen, Sam, and Hetty?), which is a really incredible moment.
After Deeks is tortured, he says he wants to get away from everything, Kensi concludes he also means everyone and is a bit devastated considering he gave her a Big Damn Kiss before he was tortured. Then Deeks follows up with this.
Deeks: Kens? (clears his throat) Hey, I just want you to know the place I went to in my head, to stop the pain...was you. I just kept thinking about your smile and your laugh. Everything. It's the only thing that got me through. For whatever it's worth.
Immediately following that...a team moment with all the agents. (Deeks was tortured dentally, by the way)
Hanna: Deeks, got you a present. *cue wind up teeth toy*
Deeks: Wow, that is, um.....
Hanna: What? Too soon?
Deeks: It might be a little too soon.
Callan:(wearing deformed teeth) So then this isn't cool?
Deeks: No, that's amazing actually.
Yet another from that same episode. Sam has a serious talk with Deeks in the hospital, saying that he'll always owe Deeks for protecting Sam's wife under torture and that he thinks Deeks is a good cop.
In a continuation of above, since then Sam has treated Deeks with a great deal more respect than ever has before.
And again, from the same "Deeks recovering from the effects of torture" plotline: Kensi brings him food and insists he watch a scary movie with her, but he just drifts off to sleep on the couch beside her before the film even starts. After having major insomnia for the past several days, the fact that he finally calmed down enough from her blabbering on about the movie may have you reaching for your insulin and loving the whole thing. Especially telling is the seemingly incoherent mumbling as he's drifting off: "It's a love story." This could be taken as him trying to respond to her ranting about the movie, or it could be taken as him finally answering Nate's question (he did say Deeks would be able to sleep when he finally admitted to himself what was different about his relationship with Kensi from his relationship with any other member of the team).
In "Neighborhood Watch" Kensi and Deeks have to go undercover as a married couple. When questioned about how they met, they tell the truth (the MMA gym in "Hand-to-Hand", Deeks first appearance) right down to what the other was wearing.
"Merry Evasion." Kensi has been sent on a long term covert op out of the country (Real Life Writes the Plot, her actress was pregnant). None of her team members know where she is or when she'll be back, only that the mission is critical and dangerous. As a Christmas gift Hetty sends her a secure satellite phone with 2 numbers programmed in and warns her never to let the phone out of her sight, that it is Kensi's lifeline. One of these numbers calls Hetty directly. The other number calls Deeks.
"War Cries" has a nice one. Nell has just come very close to being Curb Stomped in the boathouse by a witness that turns out to be the bad guy. As she is walking back into Ops sporting stiches and bruises, she has Deek's hoodie wrapped around her.
Can't remember the episode's name, but it involved a young Arabic man who was eager to become an American citizen. After he helps the team foil a terrorist attack on a ceremony to induct hundreds of new citizens, Hetty calls in the presiding judge to personally administer the Oath of Allegiance. The citizen-to-be immediately recites the oath from memory without any help. The look on the judge's face is what sells it.
That episode would be "Allegiance", Episode 13 of Season 5.
"Humbug" When commitment-phobe Kensi works up the courage to tell Deeks that she wants them to be together and Deek's response is another Big Damn Kiss.
The end of "The Seventh Child," where the boy who was brainwashed into becoming a suicide bomber and narrowly saved by Callen finally meets his long-lost family.
"Matroyshka Part 2" Callen not only finds out his real name but meets his father.