How do I securely transfer files from one UNIX / Linux server to another UNIX server using Windows or Linux desktop clients without using ftp client?
You need to use secure sftp or scp client for Windows XP / Vista / 7. Under Linux or Apple Mac OS X desktop you can use regular OpenSSH scp / sftp client to transfer files.
Windows SSH Client
Linux / UNIX / OS X SSH scp Client Examples
Use the following command from the server to which you want the files to go. In this example, transfer all files (/var/www/html) from remote server called server1 to local directory called /backup:
scp -r user@server1:/var/www/html/ /backup
In the following example, transfer all files (/var/www/html) from remote server called server1 to another server called server2:
scp -r user@server1:/var/www/html/ user@server2:/var/www/html/
Say hello to rsync
I recommend using rsync command which will only push or download updated files. It can copy locally, to/from another host over any remote shell, or to/from a remote rsync daemon. In this example, copy files from remote server called server1 into /backup directory:
rsync -avz -e ssh user@server1:/var/www/html /backup