The very first chapter Lelouch sees parallels in young!Matsumoto's behavior with Nunnally, and his Big Brother Instinct naturally kicks in, such as letting her sleep with him after having a nightmare.
Chapter 13 has Lelouch say to Soifon with regards to their friendship "While I may not always be worthy of your friendship, I shall always value it."
Chapter 14 when canon changes dramatically by having Soifon decide to go with Yoruichi. Soifon brings up Yoruichi's promise to her and gets a pat on the head.
The end of chapter 16. Yuna tells Lelouch to come back to 10th Division with her saying that it's his home.
Most of chapter 18 where the Lelouch/Yuna shipping is concerned. More specifically the dancing between them and Yuna laying her head on Lelouch's shoulder afterwards only for the chapter to end with them kissing each other.
Byakuya's proposal to Hisana (some fans have actually said the chapter feels like a case of Tastes Like Diabetes.)
Chapter 24 during the All Just a Dream segment, Lelouch is unsurprised that no one has come to see him in recovery. Later, when he wakes up for real Hisana, Byakuya, Rangiku, Shisato, Naomi, Nemu, Vera, Ryou, Isshin, Kendra, Stefan and Kukaku are all at his bedside and at the end of the chapter Lelouch realizes he actually has friends he can trust.
At the end of chapter 28 seeing Lelouch being so nice to Vera due to her PTSDMissing hand and missing eye and comforting her skittishness and telling her how good he's been to her going out of his way to give her a family.
Chapter 30, Lelouch pulling Momo out of her Heroic BSoD after he and the phantoms murder the Atrumier family.
Hisana and Rukia finally managing to come to terms with each other.
Orihimes attempts to calm half-hollow Ichigos berserk rampage are easily this
Yumichikas interactions with Shisato after Ikkakus death definitely qualify as well
When Hisana kisses Byakuya's cheek and tells him that she's pregnant and follows up with "Happy Birthday Byakuya-sama".
Everything involving Ichigo and his nakama from his dad telling him that hes just going to be his dad from now on he lost his powers AGAIN, to Kukaku saying theres always an extra bedroom at the Shiba manor to Ichigo saying to Lelouch he knows who to call on if he needs assistance.
When Ashido, Nemu, Byakuya, Kukaku, Yosei, and Susanna all pile into the archives to finish Lelouch's plot to Take down the Central Forty Six while he's asleep in the corner. It really shows how close knit of a bond Lelouch has with his allies.
Ichigo telling Orihime that shes his girl. (though the Ichigo X Rukia fandom is probably hissing and shouting big noes)
Ichigo breaking free from his seal and the first thing that happens is his reunion with Orihime.
Byakuya revealing in the Aizens Revenge arc that hes alive and well and explaining that he thought he would have to defend the lesser nobles from Aizens group, but they all banded together and helped him to live
The Reveal that the woman in crimson armor, claiming to be Ritas herald, is the spirit of Mari Akari. The following scene doubles as a Tear Jerker as well. The fact that Ichigo is crying, though he denies it, should be an indication as to the effect the scene is meant to have on the reader.
Continuing from that same thread, her reunion with Yuna the very next chapter is equally heartwarming.
Rita telling Unohana that shes very proud of her and always has been. Dawwwww
Any moment between Rita and Unohana in chapter 133. More than one fan has said the chapter should be renamed Unohana and Rita's Mother/Daughter Bonding Time. Some scenes do borderline Tear Jerker as well.
Nonette showing up to help Cornelia during the Black Rebellion and leaving an uplifting voicemail to keep her from reaching Despair Event Horizon. Nonette really is Cornelias best friend.
A meta-example. The author had considered reworking the ending scene of ch 163by breaking up Susanna and Lelouch so that Lelouch could be with Shirley. The heartwarming part comes from the number of positive reviews of people liking the pairing and wanting him to keep it. He has said he's felt moved by such things. Thus changing it into a One True Threesome.
Kasumi putting her trust in a single person: Ichigo.
On top of Ichigo saying to her that shes been his friend since she helped rescue his sister.
And her falling asleep, using him as a pillow. As she herself notes, it's the first time she's never had to keep one eye open.
Cornelia and Marianne's scene in chapter 198 is really moving.
In chapter 200 Rita and Kasumi's moment really gives this feeling.
From being deader than a doornail to suddenly being alive and well, considering Lelouch shows up at his own funeral, dressed as Zero, it really breaks the miserable tone and sets it to both a heartwarming one and an awesome one. And then later that same chapter, years into the future he becomes is a daddy.
The Stinger; Rita's loyalty has always been to Feluca, not Soul King, and putting Feluca in charge, and with it the promise of a better world, must count.