SSH or Secure Shell is a secure method of accessing your web server for manipulation or file transfer (using SCP or SFTP). Here are a few software applications that you can use to access your server via SSH.
OpenSSH is the primary SSH client and server used for Linux, BSD, Mac OS X and other Unix-like operating systems. It is free and open source and is part of the OpenBSD project. It includes scp and sftp for secure file transfers.
Although it works with both Windows and Unix, Putty is mostly used by Windows users, since SSH is not installed on Windows by default (unlike Linux and Mac OS X). PuTTY is free and open source.
Filezilla is a file transfer application that includes support for scp and sftp. It is free, open source, and has cross-platform support.
A GUI file transfer program, WinSCP supports scp and sftp, and it is core is based on PuTTY. WinSCP is free and open source.
Cyberduck is a file transfer application for Mac OS X that supports SFTP. It is free and open source software.