From the web site:

* wm-oldmenu2new is a script to convert from old-style Window Maker menu
  file to the new PropertyList style of the WMRootMenu for use with WPrefs.

  Thanks to Luke Kendall and Toby J Sargeant.

Note that this script has to be run from within your home directory.
Once you've done this, you should be able to click 'Yes, Discard and Update'
within WMPrefs' Menu page to switch to the new PropList menu format.

WWW: http://largo.windowmaker.org/files.php#wm-oldmenu2new