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!

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