Adobe's popular PDF format makes files look great--at least, when the original material does--and Adobe Reader lets everyone look at the files for free. However, you can't make annotations to those documents unless someone with the full Acrobat program has saved the PDF in an editable form. If you've got a locked-down PDF, you're out of luck... unless you've got Tracker Software's free PDF-Xchange Viewer.
This attractive, easy-to-use freebie can't create PDFs, but it lets you monkey with existing ones all you like. It accepts many kinds of markup, from highlighting to circles to sticky notes. The loupe tool magnifies sections for you, letting you get a better look. You can export the product in a number of different forms--including BMP and TIFF--and (of course) you can save it as a PDF.