I would not put Workspaces into SCM; that would demand that each developer's environment be identical. Instead take care to avoid any hard-coded paths; use workspace variables.
Use Project Set Files to identify and share sets of projects that need to be imported to a Workspace. These files can/should be kept in SCM, perhaps in dedicated release projects.
My practice when doing serious work on an application is to start with a clean workspace, no extraneous projects. Populate it using the PSF.
One route people take is to generate the Eclipse projects from the build file. This has an added benefit if the development environment is designed to not have a rigid structure (e.g. the path to library X can be relatively different in environment Y than in environment Z) since the same configuration data (files, environment variables, etc) can be used to set up the Eclipse project as the non-Eclipse environment.
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