You can choose to let Subversion ignore certain resources (files or folders) in your working copy, such as derived files (e.g. .class files compiled from Java source) and other files that do not belong under version control. By ignoring them, Subclipse doesn't mark them as "unknown", and they no longer appear in the Synchronize view.
To ignore specific resources, select the file(s) and/or folder(s) you wish to ignore, and choose Add to svn:ignore in the Team menu. This will bring up a selection where you may choose how to ignore the file:
When in doubt, choose the first option ("By resource name"), since that will never ignore a resource that wasn't explicitly selected and ignored.
TODO: Add a nice pivture.