E-Verify is now back online. The USCIS has provided guidance for the creation of an E-Verify case for those employees hired during the shutdown for whom the E-Verify system was unavailable:
"You must create an E-Verify case for each employee hired during or otherwise affected by the shutdown by November 5, 2013. If you are prompted to provide a reason why the case is late (i.e., does not conform to the three-day rule), select ‘Other’ from the drop-down list of reasons and enter ‘federal government shutdown’ in the field."
Other procedures such as Tentative Nonconfirmations, Final Nonconfirmations, with regards to both the employer and employee responsibilities, were affected and discussed by USCIS in this Adobe document.