I've been searching for a while for this same solution, but am not able to find an all-in-one solution. What I have found to be useful is that the (previously mentioned) "PDF Annotator" is a great tool for mark-ups and adding annotations (especially on a tablet), but only works on PDFs. For DJVU files I have has no luck finding an anolog. However there is a nifty little program called "A-PDF DJVU to PDF" that conveniently converts the DJVU over to PDF so that I can mark it up in the PDF annotator. Both of the programs are affordable and easy to use.
BTW here is a link for the convertion software:
http://www.a-pdf.com/djvu-to-pdf/