Inori coming to help Shu escape in episode 4, promising that she'll always be his and by his side. Turns into a major Kick the Dog moment when she reveals she only said that stuff because it was Gai's plan to make Shu cooperate, and Gai knew that Shu would be easily suckered for a pretty girl saying things like that to him.
Ayase listening to Shu's feelings, telling him to cheer up and motivating him to win the mock battle the next day.
Although you're aware of the fact that it's happening in the middle of a Tear Jerker, seeing Yahiro protect his little brother during Lost Christmas can bring a smile to almost anyone's face.
Jun: Big brother, I'm scared!
Yahiro: Everything's going to be alright. Your big brother is here to protect you.
Doubles as a CMOA when you notice that they're in front of a large pile of rubble and Yahiro has a bunch of glass sticking out of his back. That right, Yahiro used himself as a human shield to defend his little brother and still managed to put on a smile and tell him that everything was going to be alright, at the age of seven.
Even though I was crying by the end of episode 12, Gai asking Shu to kill him so he and Mana can be Together in Death, and watching them disappear together.
In episode 12, when child Gai nearly fell off a bridge, and Shu pulled him back up. And Shu called him his best friend.
Yahiro: Who here on the stage will make the best leader?
Another from episode 18, only with a touch of awesome. Inori nearly rapes Shu after temporarily being possessed by Mana. A little bit later, she witnesses a vision of Mana, where Mana tells her that she is a monster and has no soul. Then Inori remembers Shu telling her that she is her own person, subtly implying that that's why he loves her. This gives Inori the strength to overcome what was essentially "The Reason You Suck" Speech from Mana.
Episode 19, when Haruka and Shu talk about their relationship, and the flashbacks are even more heartwarming.
Another from Episode 19, when Yahiro decides he's tired of abandoning others and helps Souta escape from the burning building, despite the latter's protest.
Episode 20. Shu and Souta make up after Souta assisted in the student rebellion that nearly got Shu killed and gave Gai the chance he needed to steal the Void Genome.
Souta: Shu... I'm sorry. Please stay like this. Please... Please still be my friend.
Shu: We're friends, Souta. We'll be friends for life.
Episode 21, Inori's speech.
Gai:What did Shu give you? What sort of world did he show you?
Inori:The world's sadness... and... it's beauty. Shu suffered, and doubted, and made mistakes, and he was ashamed of his ugliness... But the reason I love him is... Shu's human. He's heartbreakingly human. That's why... even though I'm only a vessel... I still got... to fall in love...
This is at the same time as Shu curing a UN soldier of his virus, further infecting himself in the process.
And another from episode 21, when Tsugumi calls Haruka 'Mama Haruka'. She, by the way, never had a family. She just refers to all of Funeral Parlour as her family.
Towards the end Ayase is about to get into the cockpit for her Giant Robot, she notices Shu behind her, smiles and asks for his help. This is extremely significant for her, as every other time in the series when she needed to get into a chair, she would always get upset and demand that everyone around her leave, as she considered it humiliating to need someone else's help just to climb into a lousy chair.
Gai's ultimate plan after being revived was a Batman Gambit that would require Shu to overcome everything he and GHQ throw at him so that he may finally put Gai and Mana to rest once and for all, because if Gai had taken a simpler solution and not worked with Daath and Keido, Daath would have revived Mana once more and started things all over again.This may seem ridiculous, but that's just how much Gai believed in Shu.
The last episode, especially the epilogue where the gang gather together to celebrate Hare's birthday.
After the final episode aired, the Guilty Crown official website's home page featured an image of the entire cast except Souta standing together happily with the words "THANK YOU EVERYONE" floating above their heads.