(defun my-quote-function (s)
  "quote special chars in string"
  (shell-quote-argument s))

(defun my-input-sender (proc command)
  "specialized comint-input-sender function with extra quoting"
  (let ((quoting-regex "my-quote(\\(.*\\))"))
    (string-match quoting-regex command)
    (let ((string-to-quote (match-string 1 command)))
      (if (null string-to-quote)
          (comint-simple-send proc command)
        (let ((quoted-string (my-quote-function string-to-quote)))
          (string-match quoting-regex command) 
          (comint-simple-send 
           proc
           (replace-match quoted-string t t command)))))))

(setq comint-input-sender 'my-input-sender)


##</code><code>##

--> echo $foo

--> echo my-quote($foo)
$foo

--> echo "This is not quoted but" my-quote("this") is
This is not quoted but "this" is

-->