Peter Maddern posted this entry about OneNote 2007 searching in the Microsoft.Public.OneNote discussion

(Note this is pre Beta2TR)

For a couple of days, searching my newly downloaded OneNote 2007 multiple 
notebooks using Windows desktop search 3 didn't work for me at all.  I was 
able to search within the page I was in but not in multiple notebooks. I 
tried every combination of actions to fix this, for example, uninstalling 
WDS3, rebooting and reinstalling as well as repairing OneNote 2007.

I did the following and it fixed things for me:-

Control panel
Indexing options
Modify
Deselected all folders except my OneNote folders (I figured that I only 
wanted to index my OneNote folders - indexing my whole hard drive was 
unnecessary and too time-consuming and in any case, I use Yahoo desktop 
search for that)
Advanced
File types
Scroll down to file type ".one"
Select "Index Properties and File Contents" in the button selection area at 
the bottom
Close

I left indexing to run overnight.

Result - full OneNote indexing now worked well and was extremely fast too!

Prior to this procedure I had selected "Index Properties and File Contents" 
and thought that this selection applied globally to all file types.  Then I 
realised you have to make that selection for each specific file type.