(Can't find a good place to insert my entire current edifice of theory elsewhere, so I'll put it as a top level comment.)
Quirrell is Voldemort is Mr. Hat and Cloak. Quirrell's ultimate goal is driving Harry permanently into his Dark Side, so as to be another Voldemort, either to rule alongside the real Voldie or to be led by the real Voldie.
Quirrell's first attempt at driving Harry over to his Dark Side was with the Dementor in the Humanism sequence. He would have succeeded, had Hermione not been there to bring him out of it. So from Quirrell's point of view, Hermione is Harry's anchor to his good side.
So then it makes perfect sense for all the events of Self Actualization and this new sequence to be Quirrel/Voldie/H&C's handiwork. Quirrell helped SPHEW win that last battle in Chapter 74 so as to paint a larger target on Hermione. When Harry came to him with his plan for that battle, he just laughed, because Harry had unknowingly come to him with a brilliant plan to further Quirrell's own goals for Hermione's doom. He poisoned Hermione against Draco (which was difficult, because Quirrell is pure evil and Hermione is pure good and he can't understand her) so as to provoke House Malfoy further.
Now Hermione is in deep trouble, just as Quirrell intended. All that remains is for something unspeakably awful to happen to her soon, which, Quirrell believes, will help do to Harry what the Dementor almost did in January.
I'd like to point out that after Azkaban, when Quirrell tries to talk Harry into his next plot, Harry refuses by citing what Hermione and Draco would say. Quirrell sits there and thinks for a really long time, and asks if Harry really cares about what they think. My guess is that right then and there is when Quirrell decides to take them out.
(The HPMOR discussion thread after this one is here.)
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. There haven't been any chapters recently, but it looks like there are a bunch in the pipeline and the old thread is nearing 700 comments. The latest chapter as of 7th March 2012 is Ch. 77.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author's Notes.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven, eight, nine.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: