As you know, transferring files over insecure connections using protocols that send the user name and password in clear text is a really bad idea. We used to support telnet, but don't anymore - use SSH! All SMTP, POP3 and IMAP connections work over SSL. For transferring files you can use SCP. This protocol is widely supported and there are a number of free tools which you can use (see WinSCP, below).
You can also use the command line scp and sftp tools that come with Putty. You're on your own if you want to use these, but there's plenty of resources which will help you.
Alex Presland