Indie and his dad's relationship. They have an odd one, but it shows Indie's still getting on well with his family.
After Scene "dies" on account of her avatars being killed by 4chan and she becomes an Empty Shell, Indie finds the letter Scene wrote to him and decides to set things right and makes Scene two new avatars of him and Scene, holding hands, because he knows that Scene's always had a crush on him and even if he doesn't return it, he knows it'll make her happy.
What makes it even better is that Indie considers practically everything "mainstream," and this includes 4chan and everything anybody else likes. He wanted to show Scene that he really does value her as a member of the company, and it works, along with stirring up a warm and fuzzy feeling in This Troper's heart.
Also, when Indie asks Scene to sway with him in one of the episodes. Scene's expression alone made This Troper's heart melt into rainbows. She just looks so happy, and it doesn't help she's freakin' adorable to begin with...
When Indie's new girlfriend has revealed all the workers, bar Intern 2, Scene, and Hip-Hop, to be posers, Indie at least insists on trying to give them a decent farewell.
Hip-Hop dropping his Jerkass Fašade in a desperate attempt to save everybody else's jobs.
Idol and Country's relationship. Whereas Idol came across as a major jerkass in the previous season, Country arriving shows her nicer side. Even better? Country shows her Undying Loyalty for her later in the series, saving the blog and getting the interview with DJ Elephant done.
Intern 2 and Scene trying to encourage Hip-Hop to stand up to Indie and embrace his being a nerd. This eventually ends with him being rechristened as Nerdcore.
Idol's farewell, which has her reconcile with Techno and Dubstep.
An example that counts both In-Universe and out. The staff do a charity drive to raise money for poor kids, so that they can appreciate music. They raised over ten thousand dollars for charity.
Country tries to persuade Scene that she would be better off at school, where she has caring friends and is getting better. Sadly, it doesn't work.
Rayna apologising to Nerdcore for not treating him properly, and also saying that he's taught her to calm down a bit and enjoy life more.
From the same episode, Techno and Dubstep healing Country... after having caused her initial injuries, but it still counts, sort of.
Indie deciding that Scene can stay on part-time while she's at school, making an effort to also be nicer to the other staff, particularly Country, whom he acknowledges as being the one who suggested the charity drive.
Nerdcore and Intern 2 saying their goodbyes is both this and a Tear Jerker, given how upset the two are to part ways.
Metal deciding that his family is more important than the band and staying with them. Then the baby finally comes.
Indie, at the wedding of Scene and Straight-Edge's avatars, says that one of his wedding gifts for the couple will be not starting an argument with Flowchart, as he doesn't want to ruin the day.
Nerdcore deciding that he can't condemn Scene to a worthless scam marriage for the rest of her life, deciding to spare her that and revealing the truth about Straight-Edge.