Should you encrypt the system databases? A finding from a STIG evaluation, CCE-19832-5 reports that the [master] database should be encrypted with a Database Master Key using an encrypted password that meets DoD standards.

This a result of an AppDetective scan; it states:


  Resource key 'database_containing_encrypted_key' not found.=[master].


I am not deliberately storing anything in the master database.

I've encrypted all user databases but my question is: do you encrypt the system databases, specifically master?  I am using TDE with SQL Server 2012.
The answer is "NO".  

When you attempt encrypt a system database, SQL Server complains: 


  Cannot encrypt a system database.  Database encryption operations
  cannot be performed for 'master', 'model', 'tempdb', 'msdb' or
  'resource' databases.


However, it's important to realize that any successful encryption of a non-system database will cause TempDB to be encrypted automatically, to protect temporary objects. In fact, even if TDE is later removed from the user database, TempDB will remain encrypted.