If you have sufficient rights, I looked with a similar
problem in the _SITE database and in the Webs table.
You can detect there the GUID of the parent and
returning to the ID field check  underneath which site
it's hanging.

You can use STSADM to create a listing of all Top Level Sites on a virtual server. Then you'll just have to compare the list  with what is in your site  directory.

You could also search for the name of the site  and find it that way.

It likely would not show up in a search either if it wasn't added to the Sites Directory, as it wouldn't be added to the Sites Directory Content Source.

Microsoft documents several of the database tables. Since you know
WHO created  it, you could query each of your content databases for
any sites  that person authored... that could help you find the
misssing site.

I think the query would be:

select
w.FUllUrl,
u.tp_login,
u.tp_title,
u.tp_email
from webs w, userinfo u
where
w.siteid = u.tp_siteId
and w.Author = U.tp_id
order by tp_title

In addition to the STSADM tool, you could use the SharePoint
Explorer tool (it's free)
www.ontolica.com/.../SharePointExplore
rHome.html

If you ahve sufficient rights on the server,you can go to manage my
virtula server from the sharepoint central administration and click on
show all servers.This would give you a list  of all the servers.