When Akira, Benitora, Shinrei, and Hotaru wake up in Yuan's house, they're baffled by how friendly Yuan's family is and the fact that they are being fed. The family reveals their connection to Hotaru: Yuan picked him up when he was very young and starving. They all consider him family, which confuses Akira because he has always seen Hotaru as a loner. But he notices that Hotaru, who is so wary of other people that he never eats food that others offer him, is casually eating rice and perfectly comfortable in his surroundings. And after he defeats Anthony, Hotaru admits that he has missed them, and though he can't go back to being the Keikoku they knew, he wants to be part of their lives again.
When the protagonists confront Tokito, Kyo is all ready to take him on. Akira stops him, saying that he will be the one to fight Tokito. Kyo tells him no, he can't leave this in Akira's hands, and says as one of his Shiseiten, Akira does not get to override him. This results in Akira quitting the Shiseiten in order to hold up his promise to Bontenmaru. Akira, who has idolized and followed Kyo since he was about eight, defies him so he can stand on his own and be his own man. There's a look of disbelief on Kyo's face for about a second, followed by him grabbing Akira's shoulder and telling him to come back alive — not as an order from Kyo to his subordinate, but an oath of trust from one man to another.
Directly after Kyo has managed to destroy the Devil Eye in Akari's hand, she breaks down crying and promises never to stop believing in the dream she has been living with him and the Shiseiten. Kyo tells her to quit believing in sappy dreams, and it looks like he's being classic Jerkass until he continues.
Kyo: You're talking about us like we're some kind of fleeting dream... but we're all real as hell, and we're here to stay.
For Akari, who has been living in constant fear of her life being torn away from her since she was a young child, this is an incredibly important thing to hear, and it's probably the most comforting thing Kyo ever says to someone other than Yuya.
When Kyo loses his humanity in the battle with the Crimson King. Yuya kisses him, snapping him back to his senses.
Akari living Hishigi's memories after his death, and learning that he truly did care about her and considered her a trusted friend. Doubles as a Tear Jerker. Special mention to this part, right after Hishigi tells Fubuki that he is appointing Akari as his imperial guard:
Fubuki: Number Thirteen? So much faith in this shaman, and you don't even know her real name? That is like you. Hishigi: I... do know her name. But calling her by it may cause me to grow too... fond of her. Hishigi: Ridiculous, isn't it? I thought I'd gotten rid of these emotions years ago. It's not like me. Fubuki, smiling: No. It is like you. Very much so. Hishigi: I find myself wondering, if only we had met under different circumstances... if we might not have become close friends.
After the final battle of the anime Kyo and Kyoshiro stand side by side. So what do they do when everyone is together again? They smile at everyone.
This being after Kyo has gotten his original body back.
When Kyo eventually fights Kyoshiro near the end of the manga. Meaning to die all along, Kyoshiro inflicts massive damage to Kyo(who's in his body) and gives Kyo his body back. When it looks like Kyoshiro's going to die. Kyo heals him.
Kyo's return from a three-year absence after he falls with the Crimson Tower. Yuya's face and the way she runs to him... perfect scene.
The final chapter of the manga is an extra that contains no dialogue and a softer art style, and in which Kyo and Yuya are living together. Their friends all come to visit, we learn about their adventures, Akira has healed enough to try fighting Kyo (he loses, of course, but it's still a great moment), and it ends with Yuya finding that everyone has written messages on Kyo's robe. It's beautifully done and a great send-off for the series.
The very end of the anime was pretty heartwarming too.