I backup those folders including its sub folders on a daily basis to easily restore PPro's Preferences, Keyboard Shortcuts, Presets from Adobe Media Encoder when needed:
C:\Documents and Settings\User Name\Application Data\Adobe\Premiere Pro\2.0

If you want to back up your own Custom Workspaces:
C:\Documents and Settings\User Name\My documents\Adobe\Premiere Pro\2.0

Backup those folders and all its sub folders and you can easily restore everything in PPro upon next install!
Community content is available under CC-BY-SA unless otherwise noted.