Google has a google-authenticator service which provides two phase authentication for different applications and services.
You can read more about it here https://code.google.com/p/google-authenticator/
For example you can install the PAM module and use it together with OpenSSH which improves security by that you now need your password and a number to login to a SFTP service.
An easy 2 minute Ubuntu setup example can be found here http://tombuntu.com/index.php/2011/10/16/google-authenticator-pam-available-in-ubuntu-11-10/
It would be great if FTPBox could support this. Other applications like WinSCP and Filezilla works great with this, but most SSH clients do not.