I'd like to setup an ftp such that my users (and some software I write) can upload documents, and have those documents saved on the server but I don't want to allow users to see the contents of the ftp folder - essentially the ftp looks empty at all times to the user.
We've had a client using the scheduled sweep method for years without issues. I'd only see it potentially being a problem on a heavily used server with multiple people intentionally dropping files with the same name.
Regardless, here's an excellent step by step procedure for setting up a blind drop ftp site on Windows 2003 using IIS: http://www.iisanswers.com/Blind_drop_ftp.htm
Depending on your FTP server it us usually as easy as giving someone write but not read permissions on the directory. This article discusses it briefly