Sorry for this late reply, but: FTP is so 20th century. Check out [link] it's secure, it support ssh key-based authentication, and it's a mounted drive, so it just on as soon as Windows starts. (For Linux there's just SSHfs, CIFSfs/SMBfs and NFS of course.)
At work (i.e. on windows) it is total commander or the builtin one that ships with webmin.
On Linux/GNOME I use Nautilus, which is the native file manager, which, thanks to FUSE, has support for a thousand of file-systems; and that even though ftp is not a filesystem but just a transfer protocol. So basically, I don't need an extra [link] there, which is awesome
Fuer hand gebastelte batches nehm ich immer noch den cmd line ftp von Windows, obwohl CuteFTP da auch einiges bietet, habe mich damit aber leider noch nicht beschaeftigt und beim Windows FTP weiss ich halt wie es geht