Yes, you should. If this file is not under version control, then you cannot create reproducable builds of the same project, because it is no longer self contained, but depends on your specific Eclipse installation and its settings.
If you import this project into another workspace (on your or any other machine), it may behave completely different, as the compiler compliance settings, the compiler warnings configuration and a lot of other stuff is suddenly missing or different. Chances are high that such a project suddenly shows warnings/errors in the new workspace, while it was completely fine before.
Note: This all also requires that you actually configure all Java related settings in the Project properties. Never use the Java compiler settings under Window -> Preferences if you want to have self contained projects.
Just to give a concrete example: If you have configured your projects compiler compliance level to Java 6, because you are using Java 6 specific features (like Override annotations on interfaces), then the project will create a lot of compile errors on other peoples machines. This is because the default compiler compliance level in every Eclipse workspace is Java 1.5, and in Java 1.5 that Override annotation is simply not allowed.
This doesn't have anything to do with whether you are developing closed source or open source, as indicated in the other answer.
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