My apology if the following is too detail oriented for HN. I've no affiliation with any of the below, just an interest in reading and researching comfortably on-screen.
I was recently looking for a PDF viewer with annotation, and found the following for Mac. Unfortunately, I'm on Windows; otherwise, this looks to be what I was after:
http://skim-app.sourceforge.net/index.html
http://openwetware.org/wiki/Skim_-_PDF_reader_and_annotation...
Skim maintains annotations in a separate file. I would imagine this also allows it to work with locked PDF's, whereas Acrobat Reader won't permit annotating such. The annotations can be merged into an updated PDF for distribution, if needed.
On Windows, the two seemingly most legitimate options I've found are both commercial products with free versions:
http://www.pdfxviewer.com/
http://www.foxitsoftware.com/pdf/rd_intro.php
These both appear to add annotations to the PDF file, and to be limited by the Acrobat permissions assigned to that file. Foxit Reader says it adds some sort of visible component to the presentation of the annotated page, unless you upgrade to the paid version.
I haven't used them, yet. (I've had some hesitation about installing them.) If anyone has better suggestions for the Windows environment, I'd love to hear them.
Noting Johnny2112's comment re MS Reader blanking the background: For blanking the screen (or graying it), donationcoder has a little AutoHotKey based hack that dims all but the focused window. It's named ghoster, and is available in both AHK script and compiled format. Recently, Spyware Doctor has balked on a few things from donationcoder, but this appears (please to check for yourself) to be a false positive against AHK -- other anti-malware products find no problem.
http://www.donationcoder.com/Software/Skrommel/index.html#Gh...