Yvaine's confession of love to Tristan while he's in mouse form.
"You want to know what the captain really said to me? He told me that my true love was right in front of my eyes... (Yvaine starts to glow)... and he was right."
The rough-and-tumble crew revealing that they've always known that Captain Shakespeare is 'a bit of a whoopsie', but that no matter what else he is, he is their captain.
Really, any moment with Tristan and Yvaine after they're taken aboard Captain Shakespeare's ship.
When Una and Yvaine are kidnapped by Lamia, and Una holds a sobbing Yvaine and strokes her hair.
There's also the scene earlier where Una steals Dishwater Sal's caravan and drives it to the Wall, just to save Yvaine from turning into a rock in the human realm (and given that Una was Sal's slave, she must have known she'd get in huge trouble for it). When Una is freed of Sal, instead of running and escaping, she stands her ground and refuses to let Lamia kidnap Yvaine. It doesn't work out so well, but it still was very kind of her.
Yvaine's reaction when Tristan shows up to save her at the witches' fortress.
The ending, when Tristan and Yvaine, having ruled Stormhold for many happy years, light the Babylon candle and return to the stars. Nothing like the ending of the book, but still... awww.
The princes seem to genuinely love their sister Una, which may or may not have to do with the fact that being female, she does not have to compete in the race for the throne. When the brothers see her for the first time after years of separation (due to Una being Sal's slave for decades), they are delighted.
Primus and Tristan's interactions, especially since they are unknowingly uncle and nephew.
Septimus seems very keen on keeping Primus alive — even though he coldly murders at least two siblings, he tells Primus to "stay in his tower" and leave the hunting for the stone to him. He doesn't care when he dies, but at the very least he respected his eldest brother.
At the coronation, seeing Dunstan and Una finally reunited.
The book
This interaction between Primus and Tristran.
Primus: When I am king, you must visit me in Stormhold, where you will sleep on silk and drink the finest wine. Tristran: My family are sheepfarmers, but if you ever pass our way, we'll give you a bed to sleep in, and woolen clothes, and all the mutton stew you can eat. Primus:[puts his hand on Tristran's shoulder] Thank you.
It becomes heartwarming when you realize that Tristan has offered to share everything his family owns with a near-complete stranger, but that it may also be the first time anyone has given Primus anything, no strings attached, just because they like him.
Victoria's My God, What Have I Done? confession to Tristran after he returns, with Tristran forgiving her. Later on, she also befriends Yvaine.
When Tristran returns to Yvaine from Wall, the following exchange occurs.
"I'm sorry," he told her. "I won't leave you again." "No," she said, seriously and with certainty, "you will not."
