OneNote 2010 will come out this year as new core application in Microsoft Office suite. My team contributes Linked Notes feature individually, which helps people to create 2-way links between notes and original document/web page.
Introduction to OneNote 2010: http://www.onenotehelp.com
Introduction to Linked Notes in OneNote: http://www.onenotehelp.com/2009/11/19/take-linked-notes-in-onenote-2010/
As people requested, I had done the FireFox support for Linked Notes(non-official bits from Microsoft) as a FF addon last year. The Google Chrome browser may be the next target application. Due to the Adobe license limitation, the Acrobat Reader plugin to support Linked Notes goes to death.
The FF addon bits will come out soon here.