I've contacted oracle with this to try and get a confirmation.
A separate Oracle Database can be installed and used as a Oracle Enterprise Manager Grid Control (OEM Grid Control) repository without additional license requirements, provided that all the targets (databases, applications, and so forth) managed in this repository are correctly licensed. This database may also be used for the RMAN repository. It may not be used or deployed for other uses."
And according to the application server licensing document,
"18.104.22.168 Management Features
All Oracle Enterprise Manager 10g Application Server Control functionality is included with each of the Oracle Application Server editions. In addition, all of the Oracle Application Server editions include Oracle Enterprise Manager 10g Grid Control, which is an integrated tool for managing your Oracle Grid and the components running on the grid. It provides an automated configuration management, provisioning, and administrative solution for managing your Oracle data center.
Grid Control includes a restricted-use license for the Oracle Database and Oracle Application Server components required to deploy Grid Control. Refer to "Restricted-Use Licensing" later in this chapter for details on the restricted-use licenses."