The scene when Magrat is exploring the royal bedroom. There's a massive bed, big enough to fit a dozen people, and it hasn't been slept in. As a child, Verence slept on straw in an attic he shared with the rest of his family. As an apprentice, he slept on a pallet in a full dorm. As a Fool, he had slept in front of his master's door.
He'd always slept in front of the door of his master. And now he was king, he slept in front of the door to his kingdom.
And finding out that Verence keeps a few dried flowers, of the kind that Magrat wore in her hair. Even though she's said to look as if a flowerpot had fallen on her head.
Mustrum Ridcully and Esme Weatherwax's childhood connection. Ridcully mentions sending Granny letters, while she denies receiving them. But there are an awful lot of letters in that box in her house...
The ending where Granny admits to Ridcully that she picked up a Flash Sideways from at least one alternate universe where the two of them married and lived to a happy old age.
"She seemed happy enough. And I ain't easily pleased."
Casanunda and Nanny Ogg. Neither one is the monogamous type, but their feelings for one another are obviously very warm and real nonetheless.
When everyone thinks Granny is dead, Ridcully is sitting with what he thinks is her dead body. It’s also implied that he stole candles for her and lilies out of the garden.
Related to that, Nanny reveals that Granny started using the "I ATE'NT DEAD" card after Magrat found her "borrowing". This leads to Fridge Brilliance: Granny doesn't give two shits about what people say of her, but she decided to use the card after Magrat ran to Nanny crying that Granny died. She really does care about Magrat.
Related, when Granny is thinking she's going to die, she ends up writing her will, and leaves her mother's clock to Magrat.
When Nanny is threatening the god, she states flat out that she’s doing it for her family.
Nanny: And I'd be a little bit sorry about that, 'cos you know I've always had a soft spot for you. But I've got kiddies, y'see, and they don't hide under the stairs because they're frit of the thunder, and they don't put milk out for the elves, and they don't hurry home because of the night, and before we go back to them dark old ways I'll see you nailed.
At one point, the Queen demonstrates to Granny the illusion she's going to use to fight Magrat: An infinitely more beautiful version of Magrat, the kind of person she always wished she could be. That's Nightmare Fuel on its own, but the heartwarming part is that Granny notes she got the illusion from Verence. It's how he sees Magrat.