I had a strange problem last week. I was trying to access the WSS portal site for one of our TFS projects. We migrated the TFS to a new domain and the portal site was working before that.
However now I’ve got the lovely “404 NOT FOUND” message. More interestingly when I tried to create a new site collection with the same name, WSS told me that the site is already created. I could not see that in the site collection list page though.
By pure luck I decided to use the command line tool stsadm to enumerate all the existing site collections. I found that my site is already created indeed, however the owner of the site was an user from our old domain. What I did is basically change the owner to the correct domain and user, again using the stsadm tool, and volla – I was able to access the TFS project portal site again.