Harry Potter and the Methods of Rationality/Tear Jerker

"Bellatrix's hands were still chained to the broomstick, so it was only a finger that came up and pointed when she said, "What is that?" Harry followed the direction of her finger and saw... nothing in particular, actually... Then Harry realized. After they'd gone up high enough, there hadn't been any clouds to obscure it any more. "That is the Sun, dear Bella.""
 * Tear Jerker: Humanism. The entirety of it.
 * Also and more so the very next chapter, Chapter 47.
 * Chapter 59.

""You went to Azkaban," Harry whispered, "you took Fawkes with you, he saw - you saw - you were there, you saw - WHY DIDN'T YOU DO ANYTHING? WHY DIDN'T YOU LET THEM OUT?""
 * Chapter 62

"Sometimes you call your brain and it doesn't answer."
 * Chapter 79.

"It should have meant something to her, should have touched her. Should have made her felt better inside, that Dumbledore, who had seemed so reluctant before, had now acknowledged her as a hero."
 * Every description of Hermionie during chapters 80 and 81. Reminding you personaly that this is an 11 year old girl that thinks she is about to be thrown to the Dementors. (AND has been magicaly convinced that she's guilty to boot!)
 * While unlikely and even if true her responsibility was greatly diminished, it's possible that she is guilty: the pureblood faction would respond unpleasantly if the Blood-freezing Curse that she was alleged to have used were beyond the abilities of a merely better-than-average first year student, or were not cast by her wand (the ability to check what spells were most recently cast from a wand showed up very early in the fic). She'd been False Memory Charmed into believing that Mafloy was planning to do something ultimately terrible, but neither the government of the UK nor the US recognizes a legal ability to kill to prevent another citizen from enacting vague and far-off harmful acts: self-defense or defense-of-others requires immediacy that Mafloy would not have presented since he wanted to challenge her again in the next morning. In short, she might well have been memory charmed (or Obliviated and then fed false information based on a previous save scum) in such a way as to believe that outright murder of someone who had just recently helped her was not only acceptable, but mandatory. The same girl that just a few chapters before could tell Light and Dark in a simple bright line. In a work by a writer who is very, very certain as to his opinions on the death penalty. So, how about that High Octane Nightmare Fuel and Tear Jerker combo?
 * Don't forget chapter 84,

"She felt nothing."

"Hermione let her head fall back to the bed, as Madam Pomfrey came and made her drink something that seared her lips like the afterburn of spicy food, and smelled even hotter, and didn't taste like anything at all. It meant nothing to her. She went on staring up at the distant stone tiles of the ceiling."