Is there a place in Central Admin where I can modify the "Web Site Use Confirmation" email that gets sent out periodically to site collection administrators?Is it possible to turn it off completely? (We don't delete any webs or site collections if they are in use or not in use so the email is pointless).Also where can I monitor all emails being sent out from SharePoint?

You can disable it in Central Administration > Application Management > Site Use Confirmation and Deletion. Uncheck the "Send e-mail notifications to owners of unused site collections" check box for the web app these sits are under. Also, in Central Admin go to the Timer Job Definitions. Verify the "Dead Site Delete" is 'disabled' Regards John Timney