Merlin using his alter-ego "Ahbraim" to be present for Alahnah's birth.
Also, one of Alahnah's names - Naimu - is very probably the modern Safeholdian pronunciation of "Nimue."
almost certainly, as Cayleb had indicated his desire to name his first child after Merlin/Nimue after Merlin saved Sharleyan from being killed or kidnapped in By Heresies Distressed. That conversation was a Heartwarming Moment in itself as a matter of fact.
How Firm A Foundation
Sharleyan, while delivering judgement to those involved in A Mighty Fortress' Northern Conspiracy, uses her Imperial prerogative to pardon those who had been threatened or duped into participating, or otherwise too angry or stupid to realize what they were getting into.
Merlin's interaction with Prince Daivyn. Especially after Irys notes that it's the most relaxed and comfortable she'd seen the poor boy in a long time.
Midst Toil And Tribulation
Pretty much every early scene featuring Prince Daivyn. Such as his and his sister's first meeting with Cayleb and Sharleyan, which begins with him running up and leaping into Merlin's arms.
The Empire of Charis mass relief effort for the Republic of Siddarmark in the wake of end of How Firm a Foundation. It's noted it was done without any hesitation (and, in fact, probably faster than was safe to avoid suspicion regarding the SNARCs) with no ulterior motive than to help out a nation in need. The political goodwill that would result is regarded as merely a bonus rather than the objective.
Merlin suspects that Nahrmahn's VR Form will terminate the day his wife dies. He has Immortality in his reach and he chooses to go into the next life with the women he loves. That's Happily Married.
The mass Mercy Kill of the 110th Cavalry, sparing them from the Inquisition's torture.
Merlin's introduction to the now fully self-aware Owl. Among other things is Merlin, to his own surprise, getting defensive on his behalf when someone else makes less than flattering remarks.
Like A Mighty Army
Using knowledge gained while researching other projects, Narhmahn and Owl successfully create a VR suit that Ohlyvya can use to visit Narhmahn in his virtual world.
Once again, any scene featuring Prince Daivyn. Even when he's not physically present. For example we learn that he and Hektor Aplyn-Ahrmahk celebrated their birthdays on the same day because they were only six days apart and Daivyn insisted they share. He also refers to Sharleyan as "Empress Sharley."
Two manufactory owners in Cherayth, one Old Charisian and one Chisholmian, have a frank discussion in which the Chisholmian, Byndfyrd Raimahnd, expresses his feelings and realization that Mother Church truly will not reform herself, which is what's necessitating this brutal war to begin with. Old Charisian Tahvys Sahndfyrd thinks about all the major business that needs discussing that night before responding that, just for now, all he needs is a hot meal, a good bottle of whiskey, and an evening of quiet conversation about something that has nothing at all to do with wars and manufactories.
The brother/sister relationship that develops between Merlin and Nimue Chwaeriaeu.