I think he meant the note that came with the Cloak that said to not trust Dumbledore since he'll take the Cloak from Harry. which he didn't, and then said:
But you and I are both gamepieces of the same color, I think. The boy who finally defeated Voldemort, and the old man who held him off long enough for you to save the day. I will not hold your caution against you, Harry, we must all do our best to be wise. I will only ask that you think twice and ponder three times again, the next time someone tells you to distrust me.
And considering that he wrote the note, and set up the mistrust in the first place...
Hence, Magnificent Bastard.
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: