Heartwarming: Harry Potter and the Methods of Rationality
Quirrell's Christmas gift to Harry. Assuming it's not a trap.
Hermione thanking Harry for defending her.
What Hermione did in "Humanism".
Harry's happy thought in Humanism.
Harry's (first) Christmas wish.
The bit where Draco calls forth a Patronus in chapter 47 through his love for his father and the memory of him holding his hand and helping him when he thought he was about to die. Say what you will about Lucius and Draco, but that love is genuine and powerful and Draco's reaction to seeing it manifest is beyond sweet.
On that same chapter: "Every life is precious, everything that thinks and knows itself and doesn't want to die. Lily Potter's life was precious, and Narcissa Malfoy's life was precious, even though it's too late for them now, it was sad when they died. But there are other lives that are still alive to be fought for. Your life, and my life, and Hermione Granger's life, all the lives of Earth, and all the lives beyond, to be defended and protected, EXPECTO PATRONUM!"
Harry's scene alone on the top floors of Hogwarts, in the last chapter before the hiatus.
"You can never have enough books. But you certainly tried. It was a really, really, really good try."
Real Life - CMoH: "Mr. Hagrid is innocent. Ridiculously obviously innocent. He is the most blatantly innocent bystander to be convicted by the magical British legal system since Grindelwald's Confunding of Neville Chamberlain was pinned on Amanda Knox." (Read the last phrase of the author's notes.)
Harry gives up all his money and goes deeply into debt to Lucius Malfoy, of all people, to save Hermione.
Quirrel is genuinely thankful when Harry arranges an event to entertain him when he is bored marking essays. Admittedly the event involved traumatising bullies with a dark ritual, but hey.
Harry is truly grateful and hugs Neville when he says he still wants to stay even after Hermione dies horribly.
Doubles as a Tear Jerker, but Hermione's final words at the end of Ch 89. Remember Harry's lecture on accountability in Ch 75?
Harry: "You could call it heroic responsibility, maybe. Not like the usual sort. It means that whatever happens, no matter what, it's always your fault."
Hermione's words to Harry fourteen chapters later? "Not your fault."
Lucius, after seeing Draco's newfound effectiveness from rationality training: "He will be the greatest Lord Malfoy that has yet lived." No hesitation, Lucius is just so proud of his son that he immediately declares Draco will be superior to him and all his vaunted ancestors.