It was mostly Played for Laughs, but Athena affectionately patting Claptrap on the head as the rocket is about to crash is nice to see, considering everyone else hates him.
The way Claptrap hugs Athena isn't only just cute, but he does it in such a way that it looks like a frightened toddler hugging his mother.
Gets even better when playing as Athena in Claptrap's DLC, she takes being in his mind very well with slight grumbling, and when he opens up about his feelings, she's one of two characters to apologize in response to his frustration and sadness, the other being Aurelia. Timothy also gets this in a way here, where, after he tells Claptrap to shut up, he drops his act and sincerely questions himself. Considering who he's meant to impersonate, it's a reminder that he's still a Nice Guy at heart.
Athena: Claptrap... I'm sorry.
Aurelia: I'm mortified. Sorry.
Timothy: Am I supposed to break character now? I'm so confused.
In the cold open, Lilith's shown to have taken over leadership of the Crimson Raiders in Roland's place, and refers to Brick & Mordecai as her two best men.
Brick: She called us her best men. That makes me feel good.
In the credits, Athena is shown shaking hands with Janey while she leaves on a rocket. Considering the incredibly awkward and hilarious interactions they have, with Janey crushing on Athena, and Athena having absolutely no clue how to react like a normal human being, this is a real big step up.
In True Vault Hunter Mode, dialogue with Tina carries the implication that Athena and Janey hooked up in some capacity, which, as mentioned before, is a huge step up for Athena (and nice for Janey, because she's genuinely the nicest person in possibly the whole series). Tales from the Borderlands does confirm this relationship, so what was witnessed in TVHM was the beginning.
In Claptastic Voyage, it is revealed that the reason Athena was working for Jack by this point (as canonically, she had already left his employ after getting him the Vault), was so she could support herself and Springs down in Hollow Point. Aww.
Another Pickle, where you discover Pickle's big sister, Eliza, is still alive, and you go and save her. The best part is when she finally refuels her jet and blasts Scavs with you, then zooms off to a long-overdue family reunion! Pickle invites you to go meet her in person, whereupon you discover that she had stolen all of his savings and most of his choice stock while he was making a second cup of tea. (He's fine with it, further proof they're family.)
Also, judging by Eliza's behavior with other people, (Being the typical Borderlands mentality of greed, sociopathy, and violence) the fact that she only took half of Pickle's savings and most of his choice stock, shows that she loves her brother too.
More impressive is this: Throughout the quest, you see this character having screwed over every person that she has come across. When she says that she needs your help to hold off the scavs while she gets the shuttle ready, and promises to help out when she can, your immediate assumption is that she's going to abandon you as soon as she is able to fly. Instead, she immediately starts firing at the scavs as soon as she takes to the air. You saved her life, and she repays the favor, even leaving you an impressively effective shotgun (With a hilarious voice-over effect) as thanks. She might be a con-artist, but she repays her debts.
When Moxxi is in her Mechanic clothes, the back of her overalls has the logo for her daughter Ellie's garage. Further showing that she loves her kids.
Athena has seriously mellowed out since General Knoxx, becoming less stoically serious all the time and showing more and more niceness and extreme awkwardness as she's got no clue how to be a normal human being.
She is very cute during the motivational poster mission, struggling to think of something badass to say. When you put them up in Dead Lift's base, she steadily starts to get more and more excited with each poster, commenting on how badass she looks. She also d'awws when you put up the emergency cat poster.
Janey takes an instant liking to Torgue when they make contact with each other, even though they're on opposite sides of the lasers vs. EXPLOSIONS debate. If you choose to keep the laser, as opposed to Torgue's EXPLOSIONS, Torgue has a momentary moment of despair, which Janey talks him out of by way of cheerfully extolling the timeless value of EXPLOSIONS.
Also, Torgue then asks Janey out, she tells him she's not interested, and his response is 'Friendzoned!' At that point, Torgue pipes up in the framing narrative, apologizing for his insensitive, misogynistic, comments back then. In a universe where sociopathy and violence are necessary to survive, it's good to see a guy with such decent values.
Jack's office on Helios is a cold, high-ceilinged affair with unnecessary fountains, holographic pictures of the company founders, and dark lighting. The whole thing was clearly designed for no other purpose than to illustrate that Jack is the highest-ranking Hyperion officer on the station...except for a small framed picture of a cheerful little girl on his otherwise empty desk.
This turns rather tragic after the main quest is finished and said picture is turned face down on the desk. Given how we know how he treated Angel.
Knoxx: "You assholes. What the hell did she do to you to deserve THAT? You order a code 64 on a village knowing full well her sister LIVED THERE? For hell's sake, she took out her own sister in all the confusion because you ordered thermal's only! You had to tie up that one last loose end just to keep her in the corp? So that's what happens when you know too much to leave, but you're too good at your job to die. When she realized what she'd done, she, uh — she got a little stabby. She's in the brig now. Probably ship her back to Atlas HQ tomorrow. God, I hate this place."
In one mission, Mordecai comments that Lilith doesn't like anyone. Her response is a surprisingly genuine "I like Brick."
On top of that, they get onto that subject when Mordecai asks Lilith what her first impression of Jack was - she states that, because he was the guy Moxxi left Mordecai for, she didn't like him.
Zarpedon is a major departure from the usually sociopathic Big Bads and Bad Bosses of Borderlands games - for starters, she decides to hold a birthday party with 'delicious chocolate cake' for one of the privates under her command. It's a surprisingly motherly gesture, one that the average borderlands villain (such as Handsome Jack) would turn into a hilarious, nightmarishly twisted occurrence, but it's exactly what it sounds like. There is also the fact that she is also an actual mother, and her leading the Lost Legion and defending the Vault, as mentioned in Don't Shoot The Messenger is explicitly saving her daughter and the universe from a horrible fate.
Zarpedon: Know that I was always proud of you, that I didn't want this for us and that we'll meet again. Lock and load honey it's a beautiful, terrible universe out there.
In the side mission "Last Request" you find the body of a soldier killed by Deadlift's lieutenant. He has an echo log asking you to inform Zarpedon, the person who's trying to kill you, about his death, kill his killer, and call some random guy a dick. Zarpedon thanks you for informing her about his death and when you finish the quest he apologizes for not being able to reward you because he's dead. Zarpedon contacts you and unlocks a weapons cache for you (and no, it's not a trap). She really does care about her people.
You won't have my mercy, but you have my respect.
During the credits, there's a picture showing Hammerlock fixing Claptrap after Jack tore out his wheel and shot him. Aww. No wonder Claptrap thinks he's his "bestest-friend."
After Jack vents the scientists Janey calls and asks Athena how she's doing. Athena is obviously conflicted over what just happened, and Janey offers to talk with her, because she doesn't like hearing her sad. The mercenary quickly stammers her thanks, obviously not used to it.
Really, everything involving Janey and Athena is d'aww worthy.
In TVHM mode, after that moment, Tina interjects, asking if Athena knew she was working for the bad guy at about this point, which gives this double whammy when it's clear Tina, unlike Lilith, doesn't hold working for Jack against Athena:
Athena: I suspected I had been for a while, but I wasn't about to leave a job half-done. Tina: Hey, I ain't judgin'. My best friend's a Bandit King. Brick: Awww.
Bizarrely, the relationship between Nisha and Janey Springs. No, they don't 'hook up', but they do end up as something like friends, with Nisha even commenting once about the possibility of them becoming 'Besties'. It's weird, and yet endearing, that one of the most evil and sadistic characters in the Borderlands universe ends up being friends with the nicest.
This is also a small Pet the Dog moment for Nisha. While she's rude to a lot of people and calls the Customs Claptrap an "officious little s**t", she forgives Janey when she hits on her and is delighted when she finds out that someone else likes killing things as much as she does. And she speaks very politely to Janey whenever she meets her.
Janey also seems to be one of the few people that likes Claptrap, even telling him she's sorry he lost his free will.
In Stanton's Liver, you can find ECHO recordings of a woman who worked as a cleaner for the Dahl garrison, whose daughter was sick with something bad enough that even Borderland's crazy medical tech couldn't cure. She's also becoming paranoid that something out there is watching her. It turns out that the "something" is the strange Eridian alien, who abruptly heals the woman's daughter and tells her to leave Elpis. In a universe as ugly and cynical as this one, this is a shining moment of altruistic kindness, and the one who did it wasn't even human.
Janey actually offers to help the Doppleganger get his surgery reversed if he ever wants it. He appreciates the offer, though he's pretty sure there's a bomb stuck in his face somewhere that will explode if someone tries to reverse the procedure.
The mission where Nina sends you off to find suitors is just sweet, due to their delighted reactions when your character informs them that Nina likes them, even if you have to attack them with elemental damage to see how strong they are. The last interaction between Timber Logwood and Nina is enough to give you the fuzzies,
If you're playing as Nisha, you'll come across another Pet the Dog moment for her-she sounds genuinely happy for them.
Nisha: I guess when love comes it just bludgeons you together anyway. Congrats!
They're both horrible people who kill for fun, oppress everyone beneath them and are gigantic hypocrites, but the scene in the credits where Jack gives Nisha her Sheriff's star is adorable.
Athena and Dopplejack's response to the kitten poster in the poster sidequest is beyond adorable.
Athena: Awwww! Doppleganger: Aw, kitty. I ruv him!
The ending of the People's Front mission. Over the course of the quest, it's been repeatedly made obvious that the white guns you're giving them are garbage and that they'll be killed in an instant if they try to use them. By the time the player finishes the quest and it comes time for The Revolution, the player will have steeled themselves for the inevitable black comedy. Instead, they turn the weapons into a surprisingly beautiful and creative flower statue which gets a permanent, prominent place in Concordia and remarked on in a not-entirely-disparaging way by the locals.
At the end of Home Delivery you plant a pair of threshers on a rocket ship and shoot them off to Pandora. While this will eventually turn out to have been a terrible idea, seeing the threshers point their tentacles up and wave them as if waving goodbye while the rocket launches is pretty adorable.
Sir Hammerlock saving Claptrap from a Bullymong in the post-credits sequence of Claptastic Voyage. The fact that he fixes him up afterwards makes it even better.
What's Claptrap's worst fear, besides stairs, and himself? Loneliness! Or at least, other people's loneliness. Granted, this probably qualifies for a different trope given various in-game revelations, but it's still sweet.
On that note, reuniting T.K. Baha with his wife, even if it's just in his subconscious.
More specifically, a Handsome-Jack-in-The-Box wants you to see what Claptrap's greatest fear is, you pull a lever a few times before it leads to T.K.'s farm, you talk to the guy, and he requests you bring him his wife's favorite flowers. Once you do he thanks you wholeheartedly and bemoans his wife's death a little. Jack-in-the-Box comes in and states that this fear is boring before Claptrap comes in and decides to bring T.K.'s wife back to make him happy. Jack-in-the-box sends enemies after you, and you defend the couple from the attack. Playing as Athena nets you some d'aww-worthy lines:
Imaginary TK Baha: Holy cow! You done did it! Thank you so much! hehehe! You are quite the little helper! Athena: (flustered a bit) I am not! You're welcome.
Claptastic Voyage features a Shout-Out to Robin Williams in the form of a shield called the MORQ. The shield has the voice of an impersonator speaking when it is picked up or when the shield takes damage. Remember that this is after the death of Robin Williams.
Aiding an imagined Felicity Rampant fight Super-ego-trap's goons off to make Claptrap accept the responsibility for helping in killing her. Doubles as a massive Tear Jerker when Superego begins to cry and ask what he did wrong.
Helping the MINAC from The Robot Revolution DLC, become less threatening to help Claptrap accept what happened. You do this by destroying the turrets, painting it pink, and replacing one of its weapons with a bubble blower. all the while it' constantly apologizing and thanking you for putting up with all the hassle.
Athena: A death machine seeking redemption?(*Beat*) Count me in.
Claptastic Voyage ends with a defeated 5H4D0W-TP giving up his functions to keep Claptrap alive after being shot by Jack. Keep in mind, it's implied that Claptrap has lost the will to live at this point.
Simultaneously a Heartwarming Moment AND a Tear Jerker: In the Claptastic Voyage DLC, 5H4D0W-TP offers Claptrap's Consciousness the power to kill everyone who ever mocked him and rule the universe. Claptrap admits that this does sound kind of cool, but declines. An astonished 5H4D0W-TP asks him why he's refusing, since his fellow Vault Hunters show him no kindness. Claptrap's response?
Claptrap's Consciousness: Because... they're my friends.
Wilhelm is the last character of the playable characters you'd expect but even he gets a moment, whenever he deploys his drones to assist him and Wolf takes down an enemy, he'll praise the attack drone calling it a chip off the old block and tell it to keep it up.