Harry's final conversation with Lasciel, where he makes her realize that she does have a choice and that she can redeem herself. And then, in the final confrontation, she accepts the psychic backlash from escaping the mind-control spell, effectively sacrificing her existence for the sake of Harry's. Redemption is, indeed, a beautiful thing.
Minor clarification: It wasn't Lasciel the Fallen, but Lash, the "shadow" living in Harry's head. Harry actually gave her a portion of his soul, and her sense of self in the process, which just makes it more heartwarming.
Even more heartwarming when you consider a certain revelation in Skin Game: the fact that this moment was such a potent act of selfless love that it gave birth to a spirit of intellect made of both Lash and Harry's souls.
The final conversation of the book between Ramirez and Harry, with Ramirez saying he's with Harry 100%, especially when Harry watches over him sleeping the whole night because "you don't leave an injured friend alone."
Molly, terrified and more than a little scarred, finally learns why Harry fights, and still steps forward to fight as well. Her father's daughter, indeed.
Glimpses of Marcone's inner good nature always end up being CMoHs. The best is in here, when Marcone is providing an extraction route for Harry and the battle gets heated. Marcone tells Harry he didn't sign on for a war. Harry responds by going up to him and saying:
"People are dying, John. Help me save them. God, please, help me."
"Who do you think I am, wizard?"
"Someone who can help them. Maybe the only one."
He stared at me with empty, opaque eyes. Then he said very quietly, "Yes."
It's a CMoH for Harry too. Earlier, when planning the operation, Harry was asked by Marcone to say "please" in return for help and it was like pulling teeth (admittedly, Marcone was intentionally being an ass about it to annoy Harry). Even when planning to take on the monsters who hurt his friends and were threatening more people, Harry has trouble saying "please" to Marcone. But when it comes to saving civilians -strangers, even- Harry has no trouble putting down his pride.
As a comparison, the only other time Harry begs is in Changes when he begs Uriel to fix his broken back so he can go rescue his daughter), and he himself admits how hard it is for him to say it.
Murphy sits Harry down, and has a calm talk with him outlining her worries about his growing anger issues and Harry (eventually) listens and admits she had a point. Considering where these two characters started, it really emphasised the trust and friendship that has grown between them.
Heartwarming in Hindsight: It may have been manipulated by Peabody, but the build-up to the Harry/Luccio ship that will emerge in Small Favor is very sweet. It's always nice when Harry can sit and chill with a friend. It's implied that he, Luccio, Ramirez, Meyers, and the twins had a pretty good time together at Camp Kaboom before the ghoul attack.