Note for future reference: To clean up your Workspace list in Flex Builder, edit org.eclipse.ui.ide.prefs and remove the old workspaces.

You can find this in Documents/Flex Builder 3/configuration/.settings (Mac) or My Documents\Flex Builder 3\configuration\.settings (Windows). Thanks to the archived FlexCoders list for the answer. Google was no help on this one.

Dear Adobe – I’d sure love to be able to name my workspaces instead of choosing them by their directory location.  Looking at a bunch of directory listings when switching Workspaces is not all that user friendly.