My absolute favorite is the Colonel Runaway scene from "A Good Man Goes to War."
Madame Kovarian: "The anger of a good man is not a problem. Good men have too many rules."
The Doctor: "Good men don't need rules. Today is not the day to find out why I have so many."
I also love the very last scene in "The Doctor, The Widow, and the Wardrobe." After running away and hiding from them for two years, The Doctor finally decides to return home to Amy and Rory, only to find out that they already have a spot saved for him at the dinner table -- that they always
have a spot saved for him at the dinner table. It's the first time, I think, that the Doctor realized that he had a family, and he cried.