I just got this from Bruce on the OneNote Test team:

It's not optimal, but it does work. I use it here at Microsoft on my Vista x64 machine.

1. Install one of the many converter programs that will allow you to output images files when you “Print”. For example, I’ve played with http://www.print-driver.com/howto/msn_pdf_to_jpg.html 
2. Open your file in the native application (ie Adobe Reader, PowerPoint, etc)
3. Print to the new printer, outputting to TIFF (multipage color)(the defaults for the example program above work just fine)
4. Boot OneNote
5. Insert | Picture and choose the TIFF image file

Done! You can now take notes over your inserted images. I should note that we won’t OCR the images (it uses the same print driver that doesn’t install under x64), so you won’t be able to search for words in the images or copy–and-paste their content. You will be able to take notes over them, view them, and so on.

Bruce

As David wrote we are aware of this problem and there will be no fix for OneNote 2007 and we plan to address this in the next version of OneNote.  I just wanted to share this with everyone!

InScribe is a fast and easy way to enter text on your UMPC or tablet PC, offering several methods of text entry, so you can find the one that is fastest for you. With InScribe, you can resize and customize your keyboard any way you want, saving new layouts or adjusting your keyboard as you work.

Yet another powertoy written by Jeff Cardon (*applause*) that will help you when you are printing a lot of documents to OneNote.  I will just let his user guide speak for itself:

Installation:

• Download from here: ONPrintManager.zip
• Run Setup.exe and follow the prompts.
• Run OneNote and click on the following button: