Specifying File Variables in emacs docs explains how to define file-local variables, which are sometimes very useful. For example to specify a custom compilation command for R package development, I use the following at the top of each R-pkg/src/* file,

/* -*- compile-command: "R CMD INSTALL .." -*- */

Directory Variables in emacs docs explains how to use a single file to define file-local variables for all files in a directory. So instead of repeating the line above in each R-pkg/src/* file, we can use the following elisp code in R-pkg/src/.dir-locals.el just once:

((nil . ((compile-command . "R CMD INSTALL .."))))

Safe File Variables in emacs docs explains that the following in .emacs can be used to avoid the annoying “do you really want to set the local variable values?” message:

(add-to-list 'safe-local-variable-values '(compile-command . "R CMD INSTALL .."))
(add-to-list 'safe-local-variable-values '(compile-command . "make jss-paper.pdf"))