Over the last couple of days, I have been marking up a PDF document for a client that I am currently working with.  How did I do this?  By using PDF Annotator.  It is a program that allows you to use your pen and save the changes back to the PDF document or to a new version of a document.  You can use a pen, highlighter, and even add pages to the PDF document.  One of the most invaluble tools for a tablet pc.