In your workspace the following file contains your workbench information:
.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml
It is possible to delete it (or edit it but that requires some fiddling around I suppose) without breaking your workspace, the file gets regenerated by Eclipse. When you delete it all workbench related settings are lost (ie all editors are closed), but your projects of that workspace stay intact.
Edit: in Eclipse 4.2 the file is
.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi