With Migration Assistant, however, which you can launch on a computer after you've reinstalled and updated OS X, you can select certain sets of data to reimport, and can omit all your settings.
Another option, is to use the aforementioned SuperDuper! or Carbon Copy Cloner to back up a volume, or software/service combinations like Backblaze or Crashplan to specific files or folders. Then you can more easily pick and choose what to restore.
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