I am trying to use System.Net.WebClient in a WinForms application to upload a file to an IIS6 server which has Windows Authentication as it only \'Authentication\' method.>
I have seen a similar issue, where the Integrated / NTLM security will only work if you are accessing the host by machine name or localhost. In fact, it is a [poorly] document feature in Windows that is designed to protect against "reflection attacks".
Basically, you need to create a registry key on the machine that is trying to access the server, and whitelist the domain you are trying to hit. Each host name / FQDN needs to be on it's own line - there are no wildcards and the name must match exactly. From the KB Article:
http://support.microsoft.com/kb/956158/en-us