The setting is accessible under the menu Window > Preferences > General > Startup and Shutdown > Workspaces:
Here I can remove a workspace from the list. The same settings page configures the number of workspaces to remember, and if eclipse is prompting for it at startup time.
Hint: If you are wondering, where these settings are stored, then see this blog post. It is inside that file: \configuration\.settings\org.eclipse.ui.ide.prefs