Removing An Obsolete Workspace From Eclipse 3.1
Courtesy EclipseZone
Eclipse is storing the workspace information in a preferences file called "org.eclipse.ui.ide.prefs". This file is located under "%ECLIPSE_HOME%\configuration\.settings" and contains a key named "RECENT_WORKSPACES". The value of this key contains a comma separated list of workspaces, more precisely the path to the workspaces. If you delete one of the entries, it'll disappear from the workspace launcher.

