If you didn't rename your home folder (which this quite often is the case)... you may have someone corrupted your Library folder or have directory corruption.
Basically, or technically I should say, most likely what has happened is that your computer can no longer access your Library folder in your User folder. So, it creates a whole new set of preferences for your user. However, because you say that you're also missing the stuff on your desktop, it sounds more like it no longer has access to the whole users folder, which includes the desktop folder. If you rename your home folder, the system freaks out and builds a whole new home folder for you, but it disregards the old one... leaving everything blank.