If you looked on the 2007 Microsoft Office system pricing site you may have noticed that OneNote didn't have an update price : ( It only listed the full price of OneNote so regardless of if you purchased OneNote in the past you wouldn't get a discount for the new version.
We heard some complaints from you all and David took care of this so that now OneNote 2007 will have an upgrade pricing available as well! It will not be available on the worldwide consumer launch of Office 2007 + Windows Vista on January 30th 2007 but some time later in '07. So if you have OneNote 2003 and want to get 2007 at an discount (upgrade pricing) please hold out for a couple months. Thanks David!