When November goes to fight Maki, we get a quadruple one. First, he gives July a note and tells him to go to that location if anything happens. Considering most people treat dolls as human-shaped surveillance equipment, the fact that he cared enough to ensure his safety really says something. Second, it turns out the note was to send July to Misaki—she's the only one November trusts, even though they barely even know each other. Third, when she asks July if he knows where November is, he just replies "Of course. I always keep track of my friends." For the normally emotionless dolls, that's really something. And finally, November goes against his rational nature and fights Maki a second time in order to avenge April.
In the original series' episode 25, we have the part where Hei has completely ruined The Syndicate's plans by choosing to Take a Third Option when given the choice between "letting the Syndicate kill all Contractors on the planet" and "destroy Japan by sealing off Hell's Gate", and the bad guys are scrambling to try to deal with this. Their boss decides he's going to pin all the blame on his Smug Snake underling and guns him down right in front of Kirihara. She calls him out and tries to arrest him, but even her Action Girl skills aren't enough to take him down... at which point Hei comes to the rescue. But the real heartwarming bit is when he's about to zap the guy to a much-deserved death and Kirihara yells, "No!" ...and Hei listens.
Also, "Kirsi..." "No. Yin."
At the end of episode 18, when the supposedly emotionless Doll that Kenji saved earlier smiles at him.
And lest we forget grizzly hard-ass Huang's character development arc. Shioko, a woman who deliberately betrayed Huang some time ago when she seduced him to get close to and kill a police officer, is targeted for assassination by the Syndicate, who orders Huang and Hei to do it. In the end Huang can't come to kill Shioko because regardless of circumstances, because he really did fall in love with her. Hei tries to help them escape, but when Shioko sees Syndicate hitmen surrounding them, she realizes they can't escape and kills herself by running in front of a truck, thus accomplishing the mission and sparing Huang.
Huang:"That isn't true...is it, Hei? Contractors don't think about suicide, do they? Hey, Shioko...Don't betray me..."
The Reveal at the end of season one, despite Hei's gigantic hatred of her, Amber still loved him all the time and wanted to make him happy by going through with her gigantic plan. He finally realises this and makes peace with her just before she dies.
The Cool Down Hug between him and Amber was also very touching. After all the vitriol from his side, Hei realises he was wrong about his girlfriend and gives the only sign of his affection for her in a very meaningful way.
Shikkoku no Hana manga has some too. After a telepath contractor disabled Hei:
Hei: Only Yin's voice snaps me right back into my senses.
Hei *hugging the bejeezus out of Yin*: Sorry I'm late.
When Harvest wanted to create a world without irrationality or emotions in chapter 32, Hei gives up and thinks about the people whose Connection he's lost such as Amber and Pai, then Yin comes out of nowhere and hugs his back.
And then there's Parcel and Champ, who jump all over the place with heart warming, funny, awesome, and tear jerker.