* pass, the standard unix password manager
https://www.passwordstore.org/.
Instead of stopping whatever I'm doing, thinking about what password I used last time something forced me to rotate, pass saves the day!
* AwesomeWM, https://awesomewm.org/.
Maybe not a program per se, anyway using easy-to-remember keyboard shortcuts instead of clicking through a gui probably saved me a few minutes here and there.
* Gentoo Portage, The Gentoo package manager.
Yea, something that compiles packages from scratch may not sound like your typical time-saver, however, back when I had to track down every dependency and compile it myself just to get whatever package working that wasn't in the current distribution package tree, this saved me a lot of time. - This of course goes for every package manager, however back then(tm) portage had the most current releases and a lot of packages not in apt, rpm, etc.
* tmux (and tmux-cssh), https://github.com/zinic/tmux-cssh/
synchronize ssh sessions, like clusterssh, not very elegant but this saved me more than once, fast synchronized change on multiple machines at once \o/
* Ansible https://ansible.com/
Make tedious boring tasks less so, specify stuff in yaml once, execute and forget about them.