The Mezzanine

This certainly already exists for Windows and is called PDF Annotator. I use it all the time in the classroom. Most textbooks now come as a PDF as well as text and this allows me to scribble all over it (using my tablet projected onto the whiteboard at the front of the class). It's really great 'cause it has not just pens but highlighters, stamps etc. :-)

It's only $70 to buy but AFAIK there's no version of this particular program for Apple platforms.