I have mostly replaced all command line stuff with Emacs, but there are still a few CLI utilities that I continue to use, whether I am in the CLI directly or whether I am using Emacs:

• tmux or screen (terminal multiplexing)
• bash (shell scripting)
• grep, sed (filtering, formatting)
• ps, pgrep, pkill (process control)
• ls, find, du (filesystem search)
• ssh, nc, rsync, sshfs, sftp (remote access, file transfer)
• tee, dd (pipe control)
• less, emacs, diff, patch, pandoc (text editing)
• man, apropos (manual)
• tar, gzip, bzip2, xz (archiving)
• hexdump, base64, basenc, sha256sum (data encoding, checksums)
• wget, curl, (HTTP client)
• dpkg, apt-get, guix (package management)
• mpv (media player)
• ldd, objdump, readelf (inspecting binary files)
• zfs (maintaining my backup filesystem)