Carlos from the IIS team announced the IIS SEO toolkit supports querying sites with Basic or Windows Authentication. I was looking for support against Sharepoint and protected sites. This tool hasn't gotten enough press and is a original piece of software released by the IIS Team
A person I work with was looking to control web.config inheritance in sub-folders within a website. Through some research, asking on an geek mailing list, here is three options that came out. Two are IIS based , one is using ASP.NET. Hope this helps
FTP is looked at as an old tool but it works miracles if you know how to use it.