Mentioned previously, I use PDF-XChange Viewer as my PDF viewing and markup program. By markup, I mean highlighting and commenting on papers for future reference. Couple that with the ability of Google Desktop or Windows Search Service, and I have a system where I can find many things easily.
When I come across locked PDFs that do not allow for commenting (or copying text) and I really really want to comment for future reference, I use the free service provided by the website FreeMyPDF.com to unlock the file. To give you an idea of the type of things that a PDF can restrict you from doing, see the image of the “Document Properties…” dialog box from PDF-XChange Viewer here:
The FreeMyPDF.com site has a simple interface that allows you to update a file. Just a text box and a browse button allowing you to specify the location of the PDF.
Almost immediately after you finish uploading the file, the website will prompt you to download the unlocked version. There are other sites that does the similar thing (nitroPDF for example), and also other ways to do it (using pdf2ps and ps2pdf in Linux). But this works for me and it’s simple. Here is an example of the type of commenting I like to do:
As a side note, while this is perfectly fine for academic papers that you download from the web, you would not want to upload a locked PDF of a treasure map given the public nature of the site just so that you can print it out.