I have all my javascript/jquery code in a file and include it into my page. Without having apache process js files as php what would be the best way to pass data from php to
Best practice is likely as Matt mentions in the comment above: use JSON. If you're going to use jQuery, you can have a PHP script you call using either $.get() or $.getJSON(). You can find the manual for PHP JSON here: http://php.net/manual/en/book.json.php, and the API reference for the jQuery method $.getJSON() here: http://api.jquery.com/jQuery.getJSON/
HTH.