Here is an example of using wp_enqueue.
// script manager template for deregestering and registering files.
function snix_script_manager() {
// wp_enqueue_script template ( $handle, $src, $deps, $ver, $in_footer );
// deregister standard jquery
wp_deregister_script('jquery');
// loads modernizr-js script, local path, no dependency, no version, loads in header
wp_enqueue_script('modernizr-js', get_bloginfo('stylesheet_directory') . '/js/modernizr.js');
// loads jqery script, from google cdn url, no dependency, yes version, loads in footer
wp_enqueue_script('jquery', ("http://ajax.googleapis.com/ajax/libs/jquery/1.6.4/jquery.min.js"), false, '1.6.4', true);
// loads custom-js script, local path, dependency is jquery, no version, loads in footer
wp_enqueue_script('custom-js', get_bloginfo('stylesheet_directory') . '/js/custom.js', array('jquery'), false, true);
// page specific loading, no need to load everything on every page
// if it is (! - not) contact page, do not load contact-form-7 scripts
if ( !is_page('contact') ) {
wp_deregister_script('contact-form-7');
}
}
add_action('wp_enqueue_scripts', 'snix_script_manager');
At the bottom I am loading only my contact form on my contact page, no need to pull in a script on every page if it is unneeded, check Devin's site for more info on optimizing WP scripts.