I recently started using Microsoft OneNote 2007 as part of my GTD system. My GTD "hub" is still my task list in Outlook, but I do use OneNote for three purposes:
1. Capturing daily notes on the fly for future processing,
2. managing projects, and
3. storage of reference material.
I am capturing and storing stuff in OneNote, then pushing it to Outlook during my weekly reviews. OneNote serves as an inbox and as a storage location for project information and reference material.
If anyone is interested, I created a detailed description of my setup (complete with screenshots) here:
Is anyone else using OneNote in your GTD system? How are you using it?