After treating Gen like an ignorant streetrat for most of the book, the magus is sincerely regretful and concerned after Gen is severely wounded trying (and failing) to get the Attolians away so the others can escape.
Pick a moment with Gen and Irene in The King of Attolia, any moment. Odds are it's heartwarming.
"You are treasure beyond any price.”
The king lifted a hand to her cheek and kissed her. It was not a kiss between strangers, not even a kiss between a bride and groom. It was a kiss between a man and his wife, and when it was over, the king closed his eyes and rested his forehead in the hollow of the queen's shoulder, like a man seeking respite, like a man reaching home at the end of the day.
References were made at least four times in The Queen of Attolia to Gene's fear of the rumor that Attolia, if she caught him again, would "send him to the afterlife blind, deaf, and with his [lying] tongue cut out as well." Thus it's particularly heartwarming in the third book when Gene wakes from a nightmare and Irene assures him that she loves his ears, and his eyes, and "every single one of your ridiculous lies."
Similarly, any interaction between Gen and Hiero in that same book.
Relius, having sparred with the magus of Sounis for years in their capacities as The Spymaster, contemplates opening a correspondence about botany after hearing of the magus' hobbies from Gen.
This moment, from The King of Attolia:
"Am I no longer your Queen, then?"
Shocked, he whispered, "Always," breathing his soul into the word.
Phresine, Attolia's oldest attendant, shamelessly mothering Gen as he recovers from an assassination attempt.
Teleus carrying Relius out of the cell after Gen pardons him is enough, but when the warden points out he can't carry him all the way, the other guards immediately say that "He can hand him to me, then he can hand him to me."
When the Queen smiles at Costis, it warms him all the way down to his toes.
This troper melts a little at the moment in A Conspiracy of Kings when Sophos’ parents are reunited, and Sophos realizes how much his father actually deeply cares for his mother.