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If you're managing versions in an enterprise environment, it's worthwhile to check out xDM Design. This is our design management tool that lets you check in schematics and PCB's into a vault - you can manage versions, add comments, view metadeta (e.g. simulation results, percent routed, etc.), generate outputs, and so on. It also has a collaboration tool which lets you review designs from a browser - you can view the PCB from any web-connected device (phone, tablet, etc.) and add markup, do revision comparisons, etc.
If you're just managing a few versions informally, you can try Job MGMT Wizard. It will let you copy & rename a project directory to a new location while making sure all the file references are correct. DxArchiver within xDX Designer can also be useful - it uses a configuration file (DxArchiver.xml) which you can edit to customize which files are included in the archive.
You can also consider to use the iCDB Project Backup application.
It allows you to create user backups in the design and restore them.
It is also possible make them persistent so that they are not removed.
I advise this to designers when they want to do some try outs so that they can easily jump back by restoring the backup.