ReBoot/Heartwarming

Bob de-fragmenting Hex's mask in Season 3.
- There's also her agreeing to send Bob to rejoin the others.

Hexadecimal: For you, Bob... anything.

A small moment comes towards the end of "Painted Windows". As Hex lies on the floor, weakened and practically catatonic, Scuzzy immediately rushes to her side in concern.
Slash's justification for punching Gigabyte all the way back to Mainframe.

Slash: He hurt my friend.

Dot being reuinited with Cecil (whom she had presumed deleted) at the end of "To Mend and Defend".
Hack and Slash comforting each other during "System Crash" and "End Prog".
Bob and Dot's Big Damn Kiss.
Andraia in her eponymous episode, managing to escape her own game just so she could hang out with a lonely Enzo.
"BOB!" "Whoa! I think you're a little too big for that." Even after everything Enzo's been through, he's still got that little kid inside him, who wants to be close to his hero.
Captain Capacitor's kindness in helping Matrix search for Bob in the web. At one point his crew even questions what they have to gain from it and he only responds that helping Matrix is his way of repaying Dot and in doing so is more important than any valuable.
An easily missed one due to the lighting, but in End Prog, Mouse retrieves a binome girl's guardian teddy bear. Heartwarming enough in itself, that she pauses in the middle of the system's likely deletion to give her this little comfort, but this is the same style guardian teddy bear that we've seen Mainframers with since the show started - but it's GREEN. As in it's not in the image of Bob, but Enzo. Particularly heartwarming considering all the difficulty he had to go through to gain that acceptance, given that everything about him, from age to the fact that he's green instead of blue, was originally criticized.