Certificate Manager Tool (Certmgr.exe)
Using the Certmgr tool you can manage certificates through the command line. Unfortunately it is not part of a default Windows install. It is part of the SDK and .NET Framework as well.
certmgr [/add | /del | /put] [options] [/s[/r registryLocation]] [sourceStorename] [/s[/r registryLocation]] [destinationStorename]
Certificate Manager Tool (Certmgr.exe)