If Harry does not manage to find the real culprit, then how does he save Hermione from having her wand broken?
Breakout/Direct Attack on the Wizengamot / Malfoy Manor
Transfigure a one-atom line of antimatter through the earth's crust all the way to the Wizengamot or Malfoy Manor, and then a small bubble there. His wand is then touching the item to be transformed, and it will work.
Go to Azkaban and round up a few hundred dementors.
Stealth
Bringing Hermione under the aegis of a noble house
Bribery, Trade, or Begging
Harry could offer to pay Lucius Malfoy something in restitution. It couldn't just be money or an incredible favor. As the original 'Taboo Tradeoffs' paper mentions, people only get more angry when you try to do that. Harry would need an accurate model of Lucius suspecting him as Harrymort and be able to trade him something that Harrymort would consider sacred.
Trade his invisibility cloak to Lucius for Hermione's freedom. Make sure to play up that it is 1/3rd of the Deathly Hallows and thus something Harrymort considers sacre
(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: