I was speaking with Eric Mack and he mentioned his search for a program which kept track of what you highlighted. It didn't dawn on me until then that Acrobat may be an answer (though not ideal). If you've used Adobe Acrobat 7.0 before, you likely know that you can mark-up your PDF files by highlighting text, underlining text, and adding comments. By selecting a commenting option and using the comment list/summary, you can give yourself a list of every word you mark up.
Here are the basic steps:
1. In Acrobat, open the Comment Preferences
2. Select the option: "Copy selected text into Highlight ..."
3. Save the Comment Preferences
Now, when you use the highlighter to highlight text or use the pointer to hover over highlighted text Acrobat will display the highlighted text in the pop-up. These steps work equally well in Tablet/Pen mode or in traditional laptop/mouse mode.
After you make your comments and you're ready to see everything you did, you have some options.
1. Comment List: showing the comment list, well, lists the comments you made. This is where checking that box in the preferences pays off because every highlight, cross out, note and underline you did is recorded, sorted by the page number, who made the comment and when, and the text that was commented on.
2. Comment Summary: displays the comments next to the page the comments are made, or displays a sheet with only the comments which you can then print or save as its own file.
There are still many things lacking in Acrobat that the ideal "highlighted notes search" program would have, such as sorting by different colors and integration with the pen, but it's a start.
Eric, is this close? Are we getting there?
Yes, Tracy, this does the job. Thanks. Now, if I can get Acrobat to support true Digital Ink, like PDF Annotator - that would be really useful!
Detailed instructions and screen shots posted here.