The moment The Boss catches Shaundi after they fall out of a plane in the second mission of Saint's Row: The Third. He calls her his girl.
Same scene, similar sentiment.
Shaundi: You're a fucking asshole!
Boss: Yes but I'm your asshole.
The Boss and Pierce start singing "What I Got" during one of the first missions. It just comes off as one of the most memorable parts of the game because of the chemistry it generates between the two characters, trying to stay happy after Gat dies. Probably doubles as a Crowning Music of Awesome too.
Especially with Female Voice 1 (Laura Bailey) as your boss. As mentioned on Laura's page, she's clearly having a ball doing it.
What makes this better is in the second game Boss would always go after Pierce over his music, never failed. Here, s\he just rolls with it and combines CMOH with Crowning Moment of Funny.
This troper picked up the game, and when he got to this point, Boss and Pierce were still singing along to the song when he had gotten to their destination, so he just stopped the car and didn't leave it until they had finished their song.
Just how much fun they have doing this (rather than being the Jerk Ass or grim, serious, lighthearted fun) makes this not only heartwarming, but funny as well.
Viola will remenice about how Loren was like a father to her and her sister. Considering what we as players saw of him, It makes us see him in a newlight.
This is debatable, but after you beat the Deckers and scare Matt Miller out of Steelport, Killbane allowing him to leave on good terms (and even offering himself as a reference) was amusingly heartwarming.
Oleg confessing his love for Kinzie during the final mission.
Starting when you first meet her and running through the entire game, Kinzie is a paranoid shut-in that the game is one alien sub-plot away from giving a tinfoil hat. Then, when you 100% clear out Deckers territory, she gives you a call.
Boss (Female Voice 3): Hey?
Kinzie: (whispers) I ordered pancakes
Boss: Is that a... Euphemism or something?
Kinzie: Well, since we just got done running the Deckers out of Steelport, I thought I'd try to be... You know, normal.
Boss: You mean like going more than five blocks from your place?
Kinzie: Tried that. It's overrated.
Boss: Well alright. Call me if you need anything.
At one point you have the choice of killing the man who ruined Gat's funeral, or saving Shaundi. A difficult decision, but what makes saving Shaundi even more heartwarming is that "Holding Out for a Hero" starts blaring. It didn't take me long to decide who to save.
One of the biggest problems I had about the third game was the Boss not showing any emotion about Gat's death. But, it makes the scene when you meet up with Viola, and the Boss suddenly bursts "Gat's dead because of you!" as the first time he acts how you want him to.
What makes it even more Heartwarming is the Fridge Logic: Boss didn't hide his anger cause he's an ass.. he did it to show he's still a focused leader.. which, let's face it, Gat would probably prefer have happen.
In the previous mission when Viola calls the default female voice will bitch her out over Johnny, showing how heroic she had become since the second game.
At the end of the "serious ending" in SRTT, the Saints walk out of the studio after declaring Steelport a sovereign state under their rule and the Boss offers Pierce up a position of power as Mayor. It really hits you there when you consider what the poor guy's been through since SR2.
A small one, but I think it's kind of endearing whenever Generic Female Voice-Boss calls someone "sweetie".
Potential conversation if you have Kinzie and Viola rolling with you as homies:
Viola: If you washed your hair, it could be shiny too.
Kinzie: Could you show me how?
Viola: Uh... sure?
Kinzie: We're like sisters now.
In a somewhat perverse way how Shaundi has gone into a rage over Gat's death is touching. She's ditched smoking, she's ditched the merchandise driven way the Saints had become, she's ditched her love match TV show, for revenge.
Each and every time you revive a fallen homie. In SR 1 and 2, this was just pouring some beer onto them, and they'd get back up. In SRTT, the Boss bends over, and helps the injured Saint back onto their feet. Even with the giant Oleg, the Boss will put the big man's arm around his shoulders, and help him back up.
I heard at least one time comments from the Boss when they fall\s\he helps them back up, which further backs up s\he has slid from a uncaring psychopath to a extreme Anti-Hero.
A subtle one occurs when Boss and Pierce enter Kinzie's Inner Sanctum: Pierce spies a picture of the late Lin on a wall, and immediately grabs it and hides it before Boss can see. Even with all the insults, jabs and lack of respect Pierce gets, he still looks out for his caveman/woman lug of a Boss.
Gangsters in Space. In the mission Nyteblade's Return it's revealed Gat sold his likeness to make the comic and Boss calls Legal Lee to put a stop to it. Before the final mission s\he is dead opposed to the idea of a movie, much preferring to go back to the old psychpathic ways. In the good ending the Saints just roll with it and make the movie, honoring Gat's memory and actions in getting into the comic business.
During the mission "3 Count Beat Down", you're going along with Angel as he gets his luchador mask back. He knows where it is, perplexing the Boss, and leading to this (paraphrased) exchange:
Boss: If you knew where Killbane was keeping your mask, why didn't you come for it?
Angel: He broke my spirit. I no longer felt worthy of it.
Boss: What changed?
Angel: Meeting the Saints.
The Saints, through having faith in his abilities and knowledge of the Luchadores, and being willing to allow him to lead their operations against them, gave Angel the psychological boost he needed to reclaim his life after his public humiliation at Killbane's hands.
After raiding the armory Shaundi is prepared to go after Loren, not caring that the Saints are not prepared to do so. Boss reassures her that they will take care of it and talks her down.
The Heel-Face Turn of Viola. Keep in mind that just earlier in the game the Boss had killed her mentor and father figure. Viola works with you because Killbane killed her sister. She loves her sister so much that she's willing to work with the guy who killed her mentor. It makes the Shut Up, Kirk! moment over the Boss' anger about Johnny's death prettyy justified.
During a mission involving sneaking onto STAG's aircraft carrier to rescue Shaundi, the Boss has to disguise themself as Cyrus Temple. Most of the voice options use the opportunity to tease Pierce and order him around. Russian Boss (who has an obivious crush on him) on the other hand...
Pierce: You sure you got his face right?
Boss: Stay calm Pierce. There is no reason to worry.
Pierce: I'm just sayin'...
Boss: I will not let anything happen to you, Pierce.
In the final mission of Trouble of with clonesJohnny Tag and Pierce are pinned down on a bridge with the Steelport military all over them, then the Male Boss 1 comes around and yells at them very pissed: