Edis: Emacs driven indentation script
One of the pitfalls with any language using formatting constructs you're not that familiar with, is that it becomes an unreadable mess. Your code though is properly formatted, properly indented (it would be poor style for an indentation script to be badly indented itself, wouldn't it?) and even self-documenting. On every line, it's perfectly clear where we are, what's going on and how it's done.

If we're really going to nitpick, the documentation of Emacs Lisp uses the following indentation style for conditionals:

(cond ((file-exists-p filename)
        (find-file filename)
        (indent-region (point-min) (point-max))
        (save-buffer))
      (t (message "File not found (need existing file): %s" filename))))


Which slightly differs from yours, and is more in line with the rest of the language. But I can understand a preference for either.