<script type="text/javascript" src="<? bloginfo('stylesheet_directory'); ?>/js/jquery.freetile.min.js"></script>
    <script>
    jQuery(document).ready(function() {

    for (i=0;i<40;i++) {
        var w = 128 * (parseInt(Math.random() * 3) + 1) - 1,h = 128 * (parseInt(Math.random() * 3) + 1) - 1;
    jQuery('article').width(w).height(h);
    }

        jQuery('#content').freetile();
         selector: 'article';
         animate: true;
         elementDelay: 10
        });
    </script>

for (i=0;i<40;i++) {
        var w = 128 * (parseInt(Math.random() * 3) + 1) - 1,h = 128 * (parseInt(Math.random() * 3) + 1) - 1;
    jQuery('article').width(w).height(h);
    }

for (i=0;i<40;i++) {
    var w = 64 * (parseInt(Math.random() * 3) + 1) - 1,
    h = 48 * (parseInt(Math.random() * 3) + 1) - 1;

    //this part here is where the error happens.
    //you're asking to set the width and height to every element <content> on each iteration.
    //so on the last iteration, all the elements have the same width/height
    jQuery('content').width(w).height(h).appendTo('article');
}

jQuery(document).ready(function() {
    for (i=0;i<40;i++) {
        var w = 64 * (parseInt(Math.random() * 3) + 1) - 1,
            h = 48 * (parseInt(Math.random() * 3) + 1) - 1;
        $('<div class="content" />').width(w).height(h).appendTo('body');
    }
});

// What are you trying to set the width/height of?
jQuery('').width(w).height(h)

jQuery('#content .selector-for-tiled-divs').width(w).height(h)...