I know there are incredible set of tools for loading plugin classes in java, but today an idea came to my mind.
What if I have a bunch of annotated and un-annotated
It all depends on what kind of requirement you have for annotation.
Like e.g. @EJB : This annotation is designed so that container will identify and do EJB Specific work which requires scanning through files and then finding such classes.
However if your requirement is only to enable specific functionality based on annotation then you can do it using java reflection only
e.g. @NotNull : This annotation is designed in JSR 303 to verify that Annotated element is not null. This functionality can be easily implemented at run time using reflection API