EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
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. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
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, ten.
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:
You do not need to rot13 anything about HP:MoR or the original Harry Potter series unless you are posting insider information from Eliezer Yudkowsky which is not supposed to be publicly available (which includes public statements by Eliezer that have been retracted).
If there is evidence for X in MOR and/or canon then it's fine to post about X without rot13, even if you also have heard privately from Eliezer that X is true. But you should not post that "Eliezer said X is true" unless you use rot13.
There has been some speculation that Snape is H&C, but what has been lacking as far as I can tell is motive. I may have one. Cannon Snape was a Death Eater who only came over to Dumbledor's side because he wanted to try to save Lilly and then stayed on his side in order to help protect Harry out of respect for Lilly's sacrifice.
However, in chapter 27 Snape has a conversation with Harry and Snape says that he almost killed harry due to the degree that he was offended and that he gained a new understanding of what Lilly saw in Harry's father. If Snape really did have a rage inducing revelation in that conversation then that could be enough for him to abandon his role as Harry's protector. If that happened then it means that Harry, pretending to be wise, took the only thing he had left really. Snape then would have nothing to keep him on Dumbledor's side, and he knows the dark lord is returning and is destined to a fight to the finish with Harry.
I think Snape is plotting against Harry for revenge and to curry favour with the dark lord.
Snape pulled the plot with Zabini to separate Harry from Dumbledor. Snape escalated SPEW to hurt Hermione. When Snapes plan(whatever it was) was foiled by Quirrels intervention in the final SPEW battle he took the opportunity of his publicly smacking her down to memory charm her into obsession in order to set up the current plot.
ETA: From Chapter 71:
The Potions Master was frowning thoughtfully, eyes intent. "The reaction to a False Memory Charm is hard to predict in advance, Mr. Potter, without Legilimency. The subjects do not always act as expected, when they first remember the false memories. It would have been a risky ploy. But I suppose that is one way Professor Quirrell could have done it."
That's what the groundhogs day attack was all about! It was Snape figuring out the details of an effective memory charm to start the obsession without using Legilimency!
Cannon!Snape loathed Harry. Lili dumped him, if she ever liked him at all. That didn't stop him from loving her.
MoR!Snape seems to have the same kind of selfless devoted love for MoR!Lili. An 11 year old boy isn't going to change that by telling him his love isn't worthy. He already knows she didn't love him, what difference would it make to him to know why? His murderous rage at Harry's suggestion that she might not be such a great person sounds to me more like an affirmation of love than a denial of it.