We use the Secure Shell protocol for remote access, both for the commandline and for file transfer. Most times the OpenSSH client and Server are used, however we also use the Dropbear server where apropiate, because it is smaller and deemed more secure then OpenSSH.
Emacs Tramp Mode can use the SSH protocol to edit remote files.
File transfer via Rsync uses the SSH protocol
The Git (software) version control system uses the SSH protocol for distribution of versioned files.