That's helpful, thanks! I'm curious to see what other users might have to contribute.
I think the most common things here are system dependencies for R packages (libxml2, etc.). The list is very dependent on the packages being used in a given environment.
Other random tools in linux-land that I enjoy: tmux, htop, net-tools, iputils
Is there a certain problem you are trying to address? Are you just trying to be proactive / curious to see how others manage and administer the server?