There's also her agreeing to send Bob to rejoin the others.
Hexadecimal: For you, Bob... anything.
Note that he never seems anything but concerned (either for Mainframe or Hexadecimal) during this scene. He genuinely wants to help her, its not just an escape ploy. This is actually Fridge Brilliance, since in the following Season we find out that Bob was always interested in reforming viruses rather than deleting them (which was conisdered a radical view among Guardians). Makes perfect sense for him to be interested in helping her.
A small moment comes towards the end of "Painted Windows". As Hex lies on the floor in the fetal position, weakened and shaking and practically catatonic, Scuzzy immediately rushes to her side in concern.
AndrAIa in her introductory episode, managing to escape her own game just so she could hang out with a lonely Enzo. After all Enzo's frustration earlier in the episode of feeling alone with no sprites like him around the city (not to mention Bob & Dot's increasingly busy schedules), seeing the game sprite AndrAIa pull off this previously unthinkable stunt, show up in Mainframe, and hug Enzo, is an incredibly sweet moment.
When AndrAIa is near-fatally injured by a Web-Creature, Princess Bula suggests to Matrix that an energy transfusion might buy her some more time, but warns him that it "might hurt". His Response?
Matrix: Do you think I care? Do it!
"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.
Hack & Slash arguing about whether or not to delete Cyrus as ordered by Megabyte. Gives the idiot henchmen actual character and shows that they aren't truly evil (or even enjoy being mean). They liked Bob because he kept them from doing anything really bad. Referenced again as when Bob returns, Hack & Slash's first instinct is to run up and give him a big hug like he was family.
Matrix and Dot reuniting. He has the most adorable smile and her tears as she realizes her baby brother is safe and back home are just so heartwarming.
Dot and Hexadecimal searching for the Null that was Wellman Matrix so that Hex can restore his sapience. She fails at first, but when Dot begs her, she realizes that Wellman is in some sense her father as well and tells Dot, "I'll try again, Sis." Extra heartwarming as Dot and Hex are also romantic rivals and were enemies not long ago, yet Dot trusts Hex and Hex will do her best to make Dot happy.
Of course, once you remember that she referred to her and Megabyte always trying to kill each other as just sibling rivalry...