Iis – FTP Server for Windows Server 2008 – Filezilla or IIS

Depending on the server's purpose, I would eschew the native IIS FTP server in favor of a third-party server not tied to the server's authentication system. The major advantage here is that you can sandbox the accounts, and any security vulnerabilities in either the FTP server or Windows file system security are relatively decoupled. Moreover, the third-party FTP process is a little less privileged, since it isn't a core service provided by Microsoft.

A case where this would be the preferred solution would be an IIS web server where one user in each department is in charge of updating the departmental website. A case where it would not be the preferred solution is when every user in the organization has their own web space, in which case the advantages of using the central directory system would probably trump the slight security advantage.