I've mentioned GnuPG support in Emacs a number of times for encrypting documents. But it can also be used standalone via the `gpg` command.
My first contribution to GNU Guix was to get pcscd and scdaemon working with GPG, allowing me to use my Nitrokey (a USB smartcard). Those daemons typically run in the background and you don't have to worry about them.
gpg-agent can also double as an SSH agent, so you can use your smartcard in place of an SSH key on your filesystem.