(EDIT: This theory was disproven in Chap. 79)
I think Hat and Cloak is Lucius Malfoy. First piece of evidence: timing of his first appearance.
Chapter 34: Harry says "Maybe I'll just do what Draco tried with Zabini, and write a letter to Lucius Malfoy and see what he thinks about that."
Chapter 35: Hat and Cloak appears on-screen for the first time, to talk to Zabini.
Second piece of evidence: He says "Lucius Malfoy has taken notice of you, Hermione."
Hat and Cloak told Hermione "you are a Muggleborn and yet you possess a power of wizardry greater than any pureblood."
Lucius can't believe that. He can't even afford for that belief to exist, so I don't see him uttering it, even as flattery he "knows" to be false.
(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: