I would put Lucius up there as a suspect or accomplice: he loves his son, and was noticeably offended when he saw Hermione beat him in magic. Purebloods also have a history of thinking of muggleborns as not-people (see Harry and Draco talking about Luna on the train), so he wouldn't have any moral compunctions getting in the way of hurting Hermione. He was also at the school at the time, so he has almost as much opportunity as the rest of them.
And wouldn't that just be a perfect rationality lesson? Eliezer can talk about how Lucius is blinded by perceived threats to his beliefs, thereby putting his son and an innocent girl in danger.
Of course, I really hope that it's Quirrel instead, if only because it would be impossible to convict Lucius.
He was also at the school at the time, so he has almost as much opportunity as the rest of them.
He hasn't been at school during the various times H&C appeared, that we know of.
(Edit: retracted: And Eliezer's Author's Notes have confirmed that Harry explanation in the latest chapter is correct (False Memory Charm to make Hermione suspect Draco, then months of obsession, then more FMCs about the duel and Obliviating Hermione regarding the original FMC.) )
Edited to add: See comment below; I probably misinterpreted the Author's Notes. Also, I admit it's possible Lucius has been in the school without us knowing explicitly every time, since he's on the board of governors.
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: