Jarnal is an amazing software that I would donate to just because it is cross-platform, free, stable, and works.  It is unbelievable that I missed this for so long.  Now what makes this application different from Adobe Reader annotation (available when Adobe Pro gives permission to invoke feature in saved PDF) ?  Firstly it can paint the screen in freeform rather than strict text highlighting.  Secondly as a java program it has advantages for mobile devices.

Unfortunately the presentation of the website does not do justice to the power of this application.  If this application were on a flashy website it would be called 'commercialware'.

Jarnal Website - http://www.dklevine.com/general/software/tc1000/jarnal-down.htm

This tool is great for education where you want to mark up any PDF, just like the traditional hardcopy.

Give it a try and let me know what you think.

PS If you are o MAC then choose to download the DMG (a link buried on the page)