As you might have already noticed, Oracle released agents for Windows, both 32 and 64bit, and also the SQL Server plug-in. Today I'll try to briefly explain installing and configuring Microsoft SQL Server plug-in for Enterprise Manager Cloud Control 12c. I used to make use of the plug-in on 11g Grid Control and I found it as a pretty much good way of monitoring SQL Server databases especially by means of statistics collected by OEM. Besides, being able to view all of your databases -assuming you have both Oracle and SQL Server- together on a single page is very handy.

The first step is deploying agent to your Windows server. I won't get into it in detail. In a nutshell, you need install Cygwin and configure ssh service as a prerequisite and then deploy the management agent. 

Next step is deploying the plug-in:
1. Logon to OEM console. From Setup Menu navigate to Extensibility --> Self Update, click on Plug-in. Select Microsoft SQLServer Database and download it. If you can't find it in the list, most likely it is because MOS account is not configured. You can fix it by entering your MOS credentials from Setup --> My Oracle Support --> Set Credentials or Settings and re-running the UPDATE_MY_ORACLE_SUPPORT_COMPONENT_OOB_JOB job. Setting MOS credentials is also necessary to download agent for Windows.
2. When download is finished (you can select notify me option while submitting the download job), navigate to Setup --> Extensibility -->Plug-ins. Under databases, find Microsoft SQLServer Database and deploy it to your management server first then to the agent you have deployed to Windows server.

After finishing all deployments create a sql login on the SQL Server database instance to be monitored. I found that following rights is sufficient for monitoring:
  1. "View any database", "View any definition" and "View any database" on server
  2. Public role in each database, except master and tempdb, since public server role covers necessary access to them. Since login is added to model database, newly created databases from now on will also include this grant.
  3. Execute on msdb.dbo.sp_help_job stored procedure.
To add database as a target to OEM, navigate to Setup --> Add Target --> Add Targets Manually and select "Add Non-Host Targets by Specifying Target Monitoring Properties". Target type will be "Microsoft SQL Server" and choose the agent on Windows server from the list.  On the next screen fill in the Target Name, JDBC URL, Database Username (sql login you've just created) and Password of Database User. Test the connection and click OK if it succeeds.

 Below, you may find the home screen of SQL Server target.