There are methods of varying dithering/half-tone patterns in a way that is invisible to they eye but can carry enough bits of information that forensic analysis can identify an encoded printer serial number. Methods of making practically invisible changes to pure text are available too. Colour printers are starting to use these techniques instead of the (more easily noticed by the general public) extra yellow dots.

See the reply to SomeStupidPoint by schoen a few hours ago (and a couple of other posts on this thread) for more detail.