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.
The Mekakushi Dan having fun together in daze PV. Even more so when you consider the implications that it takes place after Summertime Record.
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.
Though it's a mild one, Kido instantly jumps to Kano's defense in the fourth novel when Shintarou asks if Kano might hate him despite the somewhat shady circumstances. It's quite sweet to see just how trusting of Kano she is despite their bickering.
All the moments between Haruka and Takane where life was simpler and happier and they haven't went through Unwilling Roboticisation yet. Also, when Shitaro and Ayano join their circle.
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.
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.
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
At the very beginning of Episode 11, as Shintaro sees various memories of Kuroha's victories, you can see Momo has her arms around Hibiya and is slightly in front of him, implying she tried to shield him with her own body before he killed them.
Also, 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.