Your development and deployment libraries can be combined in any way required by your project:
Hibernate EntityManager can be used with Hibernate Annotations as a full EJB 3.0 compatible persistence solution. You can fall back to Hibernate native APIs, native SQL, and native JDBC whenever necessary. Any EJB3 persistence provider may be used inside or outside a J2EE application server.

Hibernate Annotations can be used standalone, if you don't want to standardize your project on the EJB3 API, entity lifecycle, and query language. You use native Hibernate APIs and reduce the time for your object/relational mapping by switching to JDK 5.0 annotations, instead of the more verbose XML mapping files.

A full open source EJB3 container integrating many other enterprise services (clustering, HA, XA transactions, etc.) is available from JBoss, built on top of JBoss Application Server and Hibernate.

JSR-220 even defines a contract for persistence provider pluggability. So you can use Hibernate EntityManager in any EJB 3.0 compatible EJB container.
Have good times with Hibernate Persistence Manager