Ghost Story has Harry learning that Mouse is now protecting Maggie. Just the mental image is enough to make one want to sob happy tears—especially when Harry speculates that he's "probably spending half his time pretending to be a pony." And this is before we learn that the "home" that Forthill found for Maggie is the Carpenters' residence, ringed with Guardian Angels.
The most touching part is Harry watching Maggie sleeping peacefully; it shows that all of the hardship that Harry endured, all of the choices he made, did have a positive outcome.
And even more touching when you realize that this is the way Father Forthill and Michael chose to repay Harry for all the things he's done for them. Harry asked Forthill to find her a good family. He did.
And Charity further embraced it. She started the series hating Dresden for being a snarky jackass who constantly put her husband in great danger. She warmed to Dresden over the years (even considering him family) and is now willing to take it even further by protecting, raising, and loving Dresden's daughter as one of her own.
Uriel offering Sir Stuart's shade the opportunity to work for him protecting free will. Made even more poignant by the fact that Stuart turns and looks to his descendant, Mortimer, who has steadily been becoming more and more badass throughout the book, and deciding that the once-cowardly ectomancer can stand on his own, and agrees.
Minor in comparison to some of the others, but in Ghost Story, when Harry is trying to prove to Murphy and company that, yes, he really is a ghost, and yes, he really is there, Mister wanders into the room. The cat stares at him and looks shocked for a second, then barrels into him and starts purring, and Harry finds that he can pet Mister.
Doubles as a Tear Jerker, but Murphy's utter denial that Harry is dead. She refuses to believe it, despite all accounts to the opposite, and when she finally accepts it, she holds her emotions in until after everything has simmered down.
And while she's breaking down in tears, Mortimer Lindquist, cowardly ectomancer who took 50 bajillion levels in badass shields her grief and attempts to hide her so her pride is not damaged.
Harry barely even thinks before possessing Molly to help her fight off the turtlenecks.
A quiet one for Marcone. In the six months since Harry's death, he essentially built a functional monument to everything Harry stood for and fought for on the ruins of his house.
It's a small one, but the scene in Ghost Story where we get a flashback to when Harry arranged for Kincaid to kill him. Before Harry's told him what the call is about, Kincaid actually seems pretty darn happy that it was Harry calling.
Yes, we know — and Harry finds out later — that he's an utter bastard, but there's something genuinely touching about Justin Du Morne giving young Harry a baseball glove and going outside to play catch. It's all in how Harry describes it. He grew up an orphan, the only gifts he'd ever gotten were given anonymously and randomly. Seeing little Harry's joy at being given a gift that's really meant for him is enough to bring tears to your eyes.
The tiny scene that follows, where Harry recovers his magic. Jim Butcher is really coming along as a writer.
I opened my eyes, standing on a random Chicago sidewalk, immaterial and unseen. I turned my right hand palm up and focused upon that sudden kindling of light and hope, crystallized by the memory of that moment of triumph and joy. "Flickum bicus," I whispered. The fire was every bit as beautiful as I remembered.
Father Forthill's death angel in general, and not just Harry's interactions with her. By her description she sounds frightening, but she's also very patient with Harry, and promises to protect Father Forthill from all the supernatural enemies he's made in his life who may want to take him in his death. Thankfully, Forthill is saved in time and her services are not required.
Combined with Tear Jerker, there's the fact that Harry's old detective mentor Nick has hunted for missing children for decades, finding only seven of them alive ... and that he's still hunting for them.
Bob realising that Harry may still have a living body to return to, and thus may not be permanently dead. No snark or long-suffering-genius-forced-to-babysit-the-idiot routine, just genuine happiness and an enthusiastic declaration of "I'll totally help" before Harry's even had a chance to ask him. Throughout the books, a lot of attention has been drawn to the fact that Bob's nature is to simply serve whoever holds his skull without much conscience, attachment or selflessness, and Harry has often had to bargain with him to get him to be helpful, even in matters of life-and-death. Seeing this amoral spirit so sincerely and unselfishly delighted for his friend is very touching.
At the climax he attacks Evil Bob to save Harry, despite earlier stating that he is terrified of doing so because Evil Bob has a real chance of killing him. Bob not only jumps in to the fray, but deliberately sets it up so that he'll be unable to run away in order to ensure that Harry makes it out of the Nevernever without having to worry about Evil Bob on his tail.