I have the following configuration:
@Inject annotation is used for java beans(POJOs) while @EJB annotation is used for enterprise java beans. When a container inject an ejb provided by @EJB annotation to another bean it also controls that ejb's lifecycle, performs pooling for stateless beans and so on(when bean which is going to be injected is not deployed the reference will be null). If you use @Inject annotation CDI mechanism simply find and create an instance of injected resource like with new operator(if the implementation of interface which is going to be injected doesn't exist the reference will be null). You can use qualifiers with @Inject annotation to choose different implementation of injected interface.