"VIM"? But seriously, it's an interesting topic you've come up with. I'd say search (and possibly also) replace are important, especially for those that Refactor their code without a full IDE.

Second would be how to install php extensions, perhaps also PEAR packages and stuff like that.

Another useful command I tend to use a lot is "ln -s", to easily switch between versions of the website, because the documentroot points to a symbolic link.

That's all I can come up with for now. If I think off something else, I'll let you know.