Episode 5 has a rather twisted one starring Saruhiko and Misaki. At first it just looks like they're honestly trying to beat the living daylight out of each other. When Saruhiko throws the knife at Misaki you think "what an ass". But when you take a closer look he actually threw two knives, which he heated up before using (that made sure the wound wouldn't get infected), but only one connected. The other went way to the side and the wound itself was really not deep, a handkerchief was enough to bandage it. So, in other words, even though he is a crazed lunatic with certaintendencies, he is still trying to not hurt Misaki if it can be avoided.
In episode 13 it's shown again that he worries a lot about Misaki. Kuroh throws him around and then throws Misaki onto him at high speed. He's obviously in pain but the moment Misaki starts screaming because Mikoto is close to death and the HOMRA mark is hurting he completely ignores that to check on him. It's a Crowning Moment of Heartwarming and somewhat of a Tear Jerker given their personal history.
Neko running away with Shiro, seemingly as if she only cares about his safety and leaves Kuroh to face his fate with SCEPTER-4, but then later conjuring an illusion of Shiro and a fake Sword of Damocles in the stadium to distract Munakata so that Kuroh can also escape.
Neko and Shiro's first meeting. It turns out that Shiro seems to have been the first person to actually be nice at all to Neko for a long time, if ever. Once Shiro shows that he's not a threat and tries to reach out to Neko, she leaps right into his arms purring. And judging by the first episode, they were inseparable since then.
Fushimi defending Seri and later standing protectively in front of other members of Scepter4. It's a sweet sign that despite his general jerkassery (and personal history), he really does care for his comrades)
After the credits, when HOMRA joins back up with Mikoto, and Anna returns to be his side. They all walk off together, with a brief shot of Anna holding Mikoto's hand.
There are some very sweet moments between Mikoto and Anna. Mikoto lying around on the ruins of a structure he destroyed in Ashinaka. Anna tries to climb up to where Mikoto is, falls, but is caught by Mikoto just in time. He picks her up from behind the neck, like a kitten and then creates a red bubble to keep Anna warm.
At the end , Neko, Shiro, and Kuro have to leave their bombed-out dorm room to take names and rescue their friends. Kuro decides to help them of his own volition, instead of asking for orders from his dead master. Neko, despite clearly being afraid of leaving their home behind, comes as well. As they leave, Neko quietly bids their room farewell.
The talk between Mikoto and Reishi. Especially when Reishi said his reason for coming there is to "see a friend".
Shiro asking Neko if she will be his first clansman. She says he's stupid for asking because she's always been his.
Shiro talking to the Gold King, Kokujoji, one final time in decades, before he leaves.
K Radio Drama 8: Fushimi seeing Anna stuck between two vending machines, and tried to help out, even though he was unable to do anything about it in the end.
In The Movie, Anna's dream sequence involving Mikoto and Totsuka.
Anna running toward Mikoto, tearfully hugging him and calling him an idiot.
Mikoto is gentle and loving toward Anna; he caresses her cheek and comforts her with words of encouragement.
The general notion that Mikoto is at peace and together with Totsuka.
The members of Scepter 4 announcing their names and drawing their swords and respectfully making way for Anna to meet directly with Munakata. Their whole exchange was touching and it showed how mature and understanding Anna has become of the situation she has found herself in.