In the first episode, when Felix meets Sarah at the bar, the two immediately give each other a big bear hug.
Sarah thanking Alison for helping with Kira and Mrs. S. It's the nicest those two have been with each other so far.
Sarah speaking with the terrified little boy who saw Helena in episode 4.
"It's okay, darling. I'm not her."
Sarah and Kira's reunion in episode 5 is a good old fashioned "d'aww" moment. Somewhat undercut by the fact that they're being stalked.
Sarah: It's me this time.
Kira (smiling): I know!
Donnie, Alison's husband, forgiving her for going crazy on him and finally being honest with her about his affair. As of the season 1 finale, this is way Harsher in Hindsight, since he's actually just continuing his deception about his role as her monitor.
Mrs. S dropped her whole life to come to Canada because it would keep Sarah safe. She promised to keep Kira safe the same way, then hugged Sarah goodbye.
Helena's interaction with Kira. You'd expect her to kill the kid, or hurt her in some way. But no, she just wants to talk to her. Then, when she lets Kira go, Helena asks if she knows the way, because she doesn't want her getting lost. Helena is also genuinely distraught when Kira's hit by a car.
If it's possible, Helena actually looks more horrified than Sarah.
Helena calling Kira 'angel'.
Kira spotted right away the same thing her mother saw in Helena-that she's a terribly lonely, terribly broken individual who has never in her entire life known love. That hug was probably the first hug Helena has ever received. Ever.
" Helena? What happened to you?"
"...I don't know."
Felix letting Alison stay over.
Sarah putting Kira to sleep and promising to keep her safe.
Throughout episode 9, everyone's really concerned about Kira's health and asking if she's okay.
Kira asking Sarah to help Helena on her behalf.
It's more than that: Kira's first words after waking up are "It wasn't Helena's fault," followed by "She just needs your help!" Even while unconscious, she was muttering things about Helena not being a bad person.
Helena is forced to call Sarah, and instructed to set up a meeting. Instead, the only thing she asks is whether Kira is all right, and when her handler realizes she's not going to cooperate if it means placing Sarah and Kira at risk, she takes an absolutely brutal beating and allows herself to be locked in a cage so she can get in one last, desperate assurance: "It was an accident!"
When Sarah frees her, Helena gives her a tentative, broken, childlike hug and whimpers "I love you".
Sarah meeting her birth mother.
Donny, of all people, standing up for Alison when he suddenly realizes that their 'intervention' is a ridiculously condescending charade full of pretentious people who have no right to tear her down when they've all done awful things. It's the first indication of why Alison married him in the first place, and it's actually very sweet. Or was, until it turned out he has an agenda of his own.
Helena turns on Tomas when she realizes that he's going to hurt Kira if he gets his hands on her. That was all it took. A lifetime of brainwashing, years of abuse and indoctrination... and then he threatened a little girl.
He promised her Kira. He said that Kira was rightfully her daughter. She could have had her 'angel'. But she will die before she lets Kira be touched by the kind of violence and misery that Tomas brings with him.
"I didn't want to fall for you. I wasn't supposed to. But I have."
Delphine showing the first hints of not being entirely onboard with the Neolutionists' agenda.
"...Promise me Cosima's safe."
And then, very pointedly not telling Leekie anything about Kira's existence. It wasn't enough to save her, but it was an act of kindness and says a lot about her character.
Pretty much every time Cosima and Delphine interact, including everyone's favorite geek monkey going out in the middle of the night, in her underwear, to buy her girlfriend ice cream.
During her confrontation with Cosima, Delphine is nothing but apologetic, owning up to everything she's done and not offering any justification for the betrayal of trust besides that she was only trying to keep Cosima safe. The only time she grows genuinely angry is when Cosima implies that she would hand Kira over to the Neolutionists.
Cosima: Delphine, you can use me. Okay? That's fine. But don't you go near that little girl.
Delphine: I didn't, and I won't!
When asked why she bothered coming at all, Delphine's instinctive answer is "Because I... because Leekie is a liar."
When a Cosima who has had the worst possible 24 hours shows up tired and sick and fighting back tears at Felix's, she manages to choke out that Sarah was right about Delphine. Sarah, who has every reason to be furious at the lapse in judgement that could have exposed her daughter, just pulls Cos in for a long, gentle hug, and you can tell it's exactly what Cosima wanted most in the world at that moment.
The fact that 'Felix's Place' has become the default bolt-hole for clones in need. It's never exactly discussed, but it's clear that to Felix the idea of leaving Sarah's "sisters" to flounder and manage on their own when they're in danger is not even to be considered.
Felix's protectiveness towards the clones is incredibly sweet. When Delphine shows up he makes a point of trapping her in the doorway and making her as uncomfortable as possible; it drives home the fact that here, she is an outsider at best and an enemy at worst, and that in both cases she is unwelcome. It would almost be cruel, if it wasn't clear that he was only angry for Cosima's sake and that until she said that Delphine was forgiven, he was going to behave as if she wasn't.
Paul quietly telling Sarah how the Neolutionists got him under their thumb, and telling her not to give up her freedom.
Delphine's little smile when she recites Cosima's ID tag.
Their instinctive little touches, even while both of them are visibly reminding themselves that they're not a couple anymore. Cosima can't help but brush her hands over Delphine's shoulders, and vice versa. When Cosima is visibly rattled by the fact that she even has an ID tag and the reminder that her girlfriend knows it and has been watching her for ages, Delphine reaches out to touch her hip and apologizes softly.
"I'm on your side now. Please believe me... you have to trust someone."
Art's reaction to finding out that Beth killed herself and that he's been working with an impostor. Yeah, he's a Good Is Not NiceHero Antagonist, but the way he nearly begs Sarah for answers shows how much he really did care about Beth.
In 2.02, Sarah discovers that Mrs. S. and Kira were safe the whole time, hiding in the same safehouse that Sarah and Felix had stayed in when they were children. Sarah goes on a trip down memory lane, points out a spot where Felix once hit his head, and shows Kira where they had carved out "S.M. + F.D. FOREVER" on the headboard of Sarah's old bed, which Kira is currently sleeping in.
Cal slowly warming to Sarah after their falling out years ago and accepting Kira as his daughter. There's a very sweet scene when they're happily playing cards together on the porch like a normal family — until Daniel completely ruins it.
Felix giving Alison a pep talk while she's in rehab.
Pretty much all of Cal and Kira's interactions are really sweet.
An unexpected one from Rachel: Sarah breaks into her hotel room and finds tapes of a young Rachel happily playing with her parents. Cosima theorizes that Rachel was raised in a sterile, loveless, rigidly controlled environment and was taught only how to be "superior" to the other clones, but Sarah insists that couldn't be the case.
Leekie of all people having one when he goes behind Rachel's orders and continues to let Cosima and Delphine research to find a cure for the formers illness.
Helena's date with Jesse, culminating in a Big Damn Kiss. It's certainly one of her happiest and most normal moments.
Kira referring to Cal as "Daddy".
The phone conversation between Sarah and Cosima, in which Sarah looks really worried about Cosima's health, and they agree getting Alison out of rehab when they're together again.
Kira pulling out one of her baby teeth because she heard Sarah say that Aunt Cosima was sick and needed them, even though she didn't fully understand why.
Alison and Donnie spend the night reconciling after the events of the last episode and finally admit their Dark Secret to the other.
Scott telling Cosima it's an honor to be working with her.
Sarah asks Kira if she would be willing to undergo a bone morrow transplant to help Cosima and she says yes. Throughout the procedure and recovery Sarah and Felix stay by Kira's side to make sure she's okay.
Helena shows her Mama Bear side when she steps in to stop a little girl in the Prolethean nursery from being abused and it is adorable.
It's confirmed that Mark and Gracie are in love. When Hank continues abusing Gracie, Mark stands up for her and they run away together once Helena had Hank incapacitated. In the next episode they get married and start a new life together.
The season 2 finale, where Sarah, Alison, Cosima and Helena all reconvene with Kira and Felix, in his apartment, and dance like fools together. They've never gotten to be all together before this point, and it's such a stupidly happy scene, it's amazing it came out of this show.
Not to mention how even after all Helena's done, Alison and Cosima still gladly welcome her with open arms. Cosima even gives her a warm hug!
And the first thing Helena says when she sees Ill Girl Cosima is "you should not be standing". Even if she's just met her sestra, she cares about her.