1. Persist layer should be coded against interfaces so that you can switch between different implementations, like jdbc, entity beans, hibernate, jdo, etc.

public interface User extends java.io.Serializable
{
    public long getID();
   ............
}

public interface UserEJB extends EJBObject
{
   ............
}
public class UserEJBBean implements EntityBean 
{
.........
}
public interface UserEJBHome extends EJBHome 
{
.........
}

3. Web or GUI interface should be isolated too. Application/business logic should be coded in javabean or standard class, session beans should serve as glues at best, or simply out of the picture if entity bean is not used.