When Echo bonds to Boyd and then Paul, and they become her handlers.
"Everything is alright-" "-now that you're here."
When Echo hugs Boyd after her exausting and draining day of being hunted. It seemed so maternal and heartwarming. A lot of fans thought that Echo had had found her Giles. Of course being Joss being Joss..
All of the scenes between Bobby and Crystal are severely creepy, but in a strange way they're also heartwarming, because you can just tell that that is what Alpha's been looking for, that synchronicity, that finding of someone who is your equal, able to understand you.
"Belonging" (2x04): Victor and Sierra, asleep arm-in-arm and in the same pod.
Hell, the entire Victor and Sierra plot. They fall in love time after time, and no matter how thoroughly their brains are scrubbed, they find each other.
In "The Left Hand" (2x06) Topher tries to "tase" Bennett with his doll-dropping disrupter. When she asks why, he says he's checking to see if she's actually an Active, because he thinks she might have implanted herself in an attractive body that had been rendered "unengageable." Bennett's response is that such an idea is idiotic, because Actives are supposed to be beautiful and... oh. The look on her face is just perfect.
Topher and Bennett get another one in "Getting Closer" (2x11) when, after spending the entire episode acting like a Smitten Teenage Girl, Topher kisses Bennett...only to withdraw in pain from his split lip (also from Bennett), and then go back for more. This being a Joss Whedon show, however, the afterglow lasts for less than a minute.
Priya introducing young Tony to his father, Anthony, in the series finale "Epitaph Two: Return" (2x13).
Also in "Epitaph Two," sane Alpha's last gift to Echo: a hard drive with Paul's imprint, so that she can have his soul alongside hers, even though the physical Paul is dead.
Heck, all of the moments involving Alpha in "Epitaph Two." For all that he was fun in previous episodes, it's good to see him content and at peace as well.
My personal favorite?
Adelle: Well, I'm glad to see you didn't clean up.
Alpha: Eh, it spoke to the schizophrenic in me. Well, both of them, actually.
Also, Topher coming home.
At the end of season two, when Topher tells Ivy to get out while she can. He spent the last two years belittling her and treating her like a servant and then he tells her this.
Topher Brink: You get your chance, you slip out. In the real world, you can write your ticket any place you land.
Ivy: I really do want to help you.
Topher Brink: Then live! You have a remarkable brain. I think it should stay in your head. Ivy, don't become me. Go. Go!
The entire developing relationship between Topher and Adelle DeWitt. Coupled with a Tear Jerker when it reaches it's conclusion.
Dominic, of all people, gets a very subtle one at the end of "A Spy In The House Of Love" (1x9). It doubles as a bit of a Tear Jerker, since he's been revealed as The Mole and is currently on his way to the Attic.
Echo: What's in store for you... you don't have anything to smile about.
Dominic: After you beat me to a pulp, they're going to erase me... but first, they're going to erase you.
Echo: I can take care of myself.
' Dominic: I know. That's why I'm smiling. 'Cause one day, you'll be erasing them. And even after all this, they still won't see it coming.
Once a year, Topher is allowed one of the actives for a "diagnostic". He thinks it's a secret, but Adelle knows that it's an imprinted engagement for personal use, like her "Miss Lonelyhearts" sessions. And what does Topher make when he can have an Active to himself and do anything for the day? A geeky best friend, so he doesn't have to be alone on his birthday. D'awwww.
Especially heartwarming when you consider that Topher could have quite literally created anything. Sex slave, hot date for a night on the town, whatever he wanted. Once the Active's memory was wiped, no one would ever know what Topher had created. But Topher, whatever other character flaws he might have, isn't that kind of guy.
The last words in the series:
" We have time."
The truth behind Caroline abandoning Bennett in the Rossum laboratory: She intentionally got herself caught, sacrificing her freedom and ultimately her humanity, just so Rossum wouldn't figure out that Bennett was her accomplice. Bennett may have started out as nothing more than a tool in Caroline's plan, but it's clear from this scene that Caroline grew to care deeply for her.