How to add an invisible watermark to PDF documents?

Here a funny idea: Just place some watermark/copyright text on top or below of a dot or other punctuation mark. It is invisible for the naked eye if it uses the same color as the text but can be extracted using copy and paste. You can also give it a dark gray color, so you still have a chance to read it on screen.

Here some principal solution:

\documentclass{article}

\usepackage{graphicx}
\usepackage{xcolor}

\newcommand\watermark[1]{%
    #1%
    \sbox0{#1}%
    \llap{%
    \makebox[\wd0][c]{%  hor. centering
    \raisebox{.5\ht0}{%  approx. vert. centering
    \csname Gin@isotrue\endcsname% = "keepaspectratio"
    \resizebox*{.8\ht0}{.8\ht0}{% Scale down (the height is also used for the width to avoid the surrounding spaces)
    \parbox{10em}{% Allow line breaks
            \color{black!90}%  
            This PDF was created by John Doe for Jane Doe.
        }%
    }}}}%
}

\begin{document}
Text text text.

Text text text\watermark.

\end{document}

The dot will then look like this: (note the hard to see text)

How about embedding it in an image with steganography, most of the image manipulation libraries such as the GD library have routines available or you can run copies individually and use TikZ!

The message is encrypted in the yellow dots! Some color printers still do it see printer steganography

With the new version (v2.2 - still in CTAN upload process, but should be available soon) of pdfcomment you could use an 'invisible' PDF tooltip.

\documentclass{article}
\usepackage{marginnote}
\usepackage[author={Peteris Krumins}]{pdfcomment}
\begin{document}
This\marginnote{\pdftooltip{\rule{0pt}{0.5cm}\rule{0.5cm}{0pt}}{handed over to:\textCR Peteris Krumins}} is just a test sentence.
\end{document}

As soon as you hover over the 0.5cm/0.5cm rectancle in the margin the tooltip pops up. Of course you can put the tooltip in the header/footer or whereever you want.