A current theory is that it contains the Philosophers stone, its certainly more important than just a rock.
If it's the Philosopher's Stone, why would Dumbledore say it was James Potter's Rock, or that he found it in Godric's Hollow? Then again it might be a big rock from Godric's Hollow that contained the (small?) Philosopher's Stone embedded inside. But could Harry Transfigure it if he didn't correctly know its current Form, or whatever the term is? Is it even safe to routinely transfigure the Philosopher's Stone?
Which holds a terrible secret.
It also holds the hint that Dumbledore gave Lily that enabled her to come up with the dangerous potion that made her sister Petunia pretty, enabling her to marry Harry's father Professor Michael E-V. Many people think this is the fabled "single point of departure from canon". Could be important, but it's hard to see how.
But EY has specifically said that there's no single point of departure, so I'm not sure why people are searching for one. If nothing else, the Interdict of Merlin is a departure from canon(even if it took me a while to notice - it's so natural that it seemed to fit right in), and that's 1400 years into the past.
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: