The Internet is a hostile environment and security is everybody's responsibility. If you are connecting across the open Internet, then we recommend you use SSH. If the server you want to connect to doesn't support SSH, it might be worth trying to persuade the administrator to install it.
SSH (which stands for "secure shell") is a recently designed, high-security protocol. It uses strong cryptography to protect your connection against eavesdropping, hijacking and other attacks. Telnet and Rlogin are both older protocols offering minimal security.
SSH also allow you to log in to the server without having to type a password. SSH's method is much more secure, and typically breaking the security requires the attacker to have gained access to your actual client machine.
SSH allows you to connect to the server and automatically send a command, so that the server will run that command and then disconnect. So you can use it in automated processing.
You can connect from your desktop to your server via SSH protocol by using a command-line tool software called Putty or GUI SFTP/SSH Client software such as CoreFtp. Both are Free versions.