When possible, I keep all "raw" files in text format (i.e. XML/DocBook, plain text, LaTeX) in addition to rendered PDFs under version version control. Also, I try to use the Subversion repository revision number as the version number for the document.
If you can't use the automatic revision number (i.e. in a Word document), I recommend using the date of last modification. Make sure to use the date of the last edit and not the current date macro, because the current date macro will fill in whatever date it is when you print the document, which is probably not what you want. Another way to go is of course to use a traditional incremental version number, but in my experience people often have a hard time knowing which version is the latest when only seeing a number. People are usually more aware of old dates.
Having the date and/or revision number as a part of the header/footer for every page is also a big plus, that way you avoid people mixing up different versions lying around on their desks...
