While it's the type of thing that goes under the radar, there is a very moving moment when Harry is using his Sight on one of the victims of the phobophages and he turns to look at Murphy. He sees Murphy with the stains of her life as the head of SI and then: "She smiled at me, a sunny light in it, though her body's face remained a neutral mask." I missed it the first time I read through and it made me do a double take when I reread it because it conveyed faster then almost any scene in the series that Murphy is Harry's friend and loves him.
Molly's return home, from the same book. Michael's first reaction on seeing his daughter come home with rainbow-coloured hair, dressed "like Frankenhooker", covered in tattoos and with piercings in pretty much every place where it is possible to have one, is to hug her.
Michael: Harry, am I just too old?
Harry: Hey, let he who hath never stonewashed his jeans cast the first stone.
Also from the same book, the scene in which Harry finds out that the fetches have taken Molly to Arctis Tor, Mab's capital and the stronghold of literally half of Faerie. Harry states that the mission has just gotten more difficult, and he doesn't expect Thomas, Charity or Murphy to still come. Without a word, they step up to his side, willing to do it anyway. To quote Harry: "A bolt of warmth, fierce with joy and pride and gratitude, flashed through me like sudden lightning. I don't care about whose DNA recombined with whose. When everything goes to hell, the people who stand beside you without flinching- they are your family. And they were my heroes."
Later on in the same book, after rescuing Molly from Arctis Tor a weary Thomas asks Harry and Murphy why they just went through all of that. Harry and Murphy exchange a smile and draw Thomas' attention to Charity and Molly. Thomas' response: "Oh. Right."
Michael's reaction after learning that Harry was willing to take on essentially the entire White Council to protect Molly.
"Greater love hath no man," he said. "Nothing I can say would be enough. She's my daughter, Harry. Thank you."
Harry eventually reconciling with Ebenezar. It took a couple of books, but considering how difficult Harry finds it to trust someone, forgiving someone for betraying it is a really big deal for him.
By the end of the book, Harry learns Michael has known Harry has the shadow of Lasciel within him and took the coin to save Michael's youngest since the end of Death Masks. And Michael still saw Harry as family, inviting him to family dinners around Christmas, and even asks him to watch over his family when Michael is away.
And before this revelation, Harry confesses to Michael about how when he had to execute someone and how it made him feel, Michael responds by relating his own experiences and similar feelings, and then goes on to say with absolute certainty that he believes Harry is a good man. It was heartwarming enough that even Harry started to tear up. Like Harry says, Michael is good people.