Sometime ago, I had a problem with a SharePoint installation. The Event Log was populated with errors that was referring to a particular site collection that did not exist.
The problem was a site collection was deleted by the site administrator without doing this via Central Admin.
This infact affected the upgrade of this SharePoint installation to SP1. It was pain as you could see it under Site Collections List but it reports this site collection cant be deleted.
The simple solution was;
1. Goto Central Admin > Application Management
2. Select Content Databses under SharePoint Web Application Management
3. Click on the Top Level DB > scroll down and remove database
4. Do not delete DB or contents
5. Go back to Content DBs and add DB, Type the name of the one your removed to attach it again.
Voila! all orphan sites have disappeared