All the moments between Haruka and Takane where life was simpler and happier and they haven't went through Unwilling Roboticisation yet.
Ene's reason to call Shintaro "Master". Why? Because Forgotten First Meeting ensues after her, when she was still TakaneEnomoto, lost a bet after he beat her in a videogame. The deal was that if she lost she would become his servant and call him Master, but Shintaro believed it was too awkward and told her to forget about it. Even after becoming a Cyber Girl, she still remembers it and calls him Master because of it.
"...Because we're brothers." The way Seto shows genuine affection to Kano after he breaks down near the end of the fifth novel goes to show how close they, and the rest of the Mekakushi Dan, are.
It's subtle, but the interactions between the Mekakushi Dan as shown in Lost Time Memory are really sweet.
Pretty much any time you just get to see the Dan interacting casually can be considered this. When you consider what so many of them have gone through in the past, it's pretty great to see them all happy.
The Mekakushi Dan having fun together in daze PV. Even more so when you consider the implications that it takes place after Summertime Record.
Episode 11. Momo uses her powers to attract all the Mekakushi-Dan's members, which works. She also manages to cheer up poor Hibiya, who was quite depressed after the "Groundhog Day" Loop and even Kano, who was broken after all the past events and Ayano's death.
Though it's subtle, seeing Kido smiling at the thought of a group dinner in one of the episodes of the anime is pretty sweet.
One of the flashback scenes in episode 9 of the anime shows Ayano walking in on Kano drawing on Seto's face, while Seto protests, clearly upset. Kano claims he was making him the villain for their game of superheroes that day, but Seto doesn't want to be the villain. In response, Ayano grabs the marker, draws on her face, and pretends that they are members of the 'Graffiti Rangers'. Even Kido joins in, and they get Kano to draw on his face, too.
Gunjou Rain. Five and a half minutes of Shion singing her love for her daughter Marry, the only thing she has in the world, and the hope that one day, she'll be able to see the world and find love like she did. It hits Tear Jerker territory halfway through when she recalls Azami's disappearance, and her subsequent death, finishing on Marry reading her diary and beginning to cry when she realises how much Shion loved her.