Linux and Mac users can use a variety of command line tools to transfer files between their local machine and the clusters. Some common ones include sftp, scp, and rsync. Mac users can also use Fetch which is a ftp client which has a graphical user interface.
Windows users can use a variety of ftp clients such as WinSCP, CoreFTP, or the ftp client that comes with MobaXterm. SSH Secure Shell and SecureCRT also have built-in file transfer capabilities.
For large file transfers, in terms of file size and/or number of files, a good option is to use Globus Connect.