The Doctor, Benny and Ace having a big damn Childish Pillow Fight in the aftermath of a bunch of horrible stuff in Set Piece. Ace attacking the Doctor with Tickle Torture, too, and then the three-way hug.
Ace: You're giggling!
Doctor: I do not giggle!
Turns into a Tearjerker when Ace breaks down completely.
Benny crying over the Doctor at the beginning of Sleepy and him wondering if she would have kids and if so, what kind of things he'd get up to with them as a surrogate grandad. Later on, the Headbutt of Love they give each other. Honestly, the whole book has adorable moments scattered throughout.
Return of the Living Dad. The Doctor kissing Benny on the cheek at the end. *squeals of happy*
The Room with No Doors: The Doctor realising that his Seventh incarnation did not somehow "kill" his Sixth, that his past, current and future selves are all the same being, and forgiving himself for his actions as both Six and Seven.