I left OneNote not for something better, but for something that fit how I think and work today.
OneNote 2010 with SkyDrive notebook sync is awesome. You can access and edit your notebook from anywhere, even from a PC that doesn't have the OneNote app. Then when you do have OneNote, you get the ...
If this helps, it's designed for unstructured information storage, so fundamentally you use it as you'd use a notebook with the exception that organisation is something you can do ad-hoc. For example ...