Nolan and Irisa singing together in the car as they ride to the Ark in the opening. It really goes a long way to show how close the pair are.
When Irisa is shot escaping from the Spirit Riders, the way Nolan carries her and tries to jostle her as little as possible is incredibly sweet.
Stahma skillfully distracting the children of a man her husband is chastising over being late for rent. Yes, it's blatantly manipulative and very much in her own best interests, but it shows that the Tarrs don't go out of their way to cause unnecessary pain.
Christie and Alak's relationship. Considering his parents' manipulative social-climbing natures, the fact that he is so open and honest and genuinely in love with this human girl is remarkable, and seeing how happy they are together the audience can't help but smile.
On another level: Stahma and Datak frequently mention that all of their manipulation is so that their son never has to worry about the kind of brutality they live with. Seeing how Alak, even though he's very much a teenage rebel, is so easy and carefree with Christie, his parents are at least getting their wish—he really is living a life that doesn't deal in lies and deceit.
Nolan warning Tommy not to put handcuffs on Irisa becomes this in the next episode, where we learn that Irisa has a deathly terror of chains. She has thick scars on her wrists that look like they came from manacles, and she makes several references to being tortured by her parents... like hell Nolan is going to let her be put in chains, again, by people with guns that she doesn't know.
It was probably as much for Tommy's safety as it was for her. Chances are she might have killed Tommy if he tried it.
She would absolutely have killed Tommy; still, Nolan could have ordered her to stand down, and he didn't. There's cooperation, and then there's subjecting your daughter to a triggering experience, and he loves her.
"Down In the Ground Where the Dead Men Go"
Even if she is trying to manipulate Christie, it is touching that Stahma convinces her to follow her own heart rather than allow her father to determine her future.
Rafe McCawley finally letting go of his rage and sparing Ben. It doesn't work, but still.
Rafe making a deal with the Spirit Riders to return stolen land then lease it from them, the first step in mending fences between the two groups.
Nolan holding Irisa's hand at the end to help her sleep.
The gradual development of the Spirit Riders' leader. It's clear he still hates the humans, and deep wanted to allow Rynn her vengeance, but he's nonetheless able to look past that and offer a hand to them.
Sukar's discussion with Rynn about his decision to lead the lawkeepers to her, and the following montage.
Rynn: The Little Wolf has the sight. So what?
Sukar: So the gods touched her, and she in turn showed me what has to happen next.
Rynn: I'm going to prison! How can that be the correct path?
Sukar: I don't know, precious daughter. Sadly, I lack the sight.
"A Well Respected Man"
Datak getting a seat on the town council is this, in a way. Though Stahma helped him con his way in, the look on his face shows that this is the kind of respect he wants, rather than the fear he usually works with.
Amanda telling Kenya what really happened with their mother, with Kenya remarking that Amanda could've told her anytime she was "fed up with her shtakko" to shut her up. Then the two of them embrace.
Rafe admitting to Quentin that Luke occupies a spot in his heart that no one could replace... right next to the ones for his wife, Christie, and Quentin.
"The Serpent's Egg"
Nolan's rescue of Irisa when she was a child.
Tommy had spent the entirety of Irisa's "interrogation" of the Castithan who once tortured her pleading with her to stop the madness and insisting she had gotten the wrong person. And all that after she had handcuffed him to a pole and made him watch in horror, thinking she'd gone mad. Of course, Tommy then learns not only that she was right, but also exactly what was done to her.
"She was a child, you piece of shtakko!"
Tommy's awkward little confession of love at the sheriff's station later that day, when Irisa asks why he reacted as furiously as he did to learning she'd been tortured so an insane Castithan could create a 'Messiah'.
"Because you're not the only one with nightmares. And because... Um..."
In the end he doesn't even have to say anything; Irisa knows and promptly shoves him against the wall and snogs him senseless.
Rynn makes her escape... and then comes back.
"A man who risks his life for another cannot be left to die."
Amanda thanks her by immediately pardoning her past crimes and giving her the second roller.
Alak arranging to get his hands on a bunch of old vinyl records, so he could play them on his radio show for Christie. He catches her attention out of an observation window on top of the Arch, and they blow each other a kiss. It's ridiculously sweet and, for once, a completely happy gesture that their parents aren't around to criticize or influence.
"Brothers in Arms"
Nolan is willing to let Eddie collect the bounty on his head (Varus Soleptor put it at 250K) on the sole condition that Eddie tell Varus that Irisa is dead.
Nolan realizes the truth in Eddie's furious accusation that he forgot his friend's involvement in saving a young Irisa's life, and sets about remedying it.
Irisa: You want me to drink this? Nolan: We're gonna have a toast, and talk about your uncle. Irisa: I don't have an uncle. Nolan: Yeah, you do.
"I Just Wasn't Made For These Times"
Rafe having a Not So Different bonding moment with Gordon. Who comes down to the mines to kill himself because he's an Indogene sleeper agent. And he manages to convince him to not go though with it.
Gordon: Thanks for trying.
And later, Gordon reuniting with his wife. Who was still wearing her wedding ring after all the years he was gone.
"And The Bride Wore Black"
This episode is full of these kinds of moments.
The flashback were Rafe saved Datak, simply because he doesn't like unfair fights.
Christie deciding to wear the antique eye shield Stahma gave her as the "something borrowed."
Even though Christie has agreed, Stahma doesn't want her daughter-in-law to be forced to do anything, so she comes up with a compromise, and personally creates an old-Earth bridal veil.
Christie: You didn't need to do that. Stahma: I wanted to.
Rafe, instead of letting the wedding be canceled and preventing his daughter from marrying a Castithan, threatens Datak to let the wedding happen as scheduled. The reason why: Simply because his daughter, Christie, loves Alak and Alak loves Christie.
Rafe overcoming at least some of his alien racism, and altering his will to give the mines to the Irathients. Keep in mind, he did not give Christie the mines in his will to save his own hide, but he could have just as easily given it to the human population of Defiance instead.