How to Load Plugin JS in theme’s footer section

The available input parameters of wp_enqueue_script() are:

<?php wp_enqueue_script( $handle, $src, $deps, $ver, $in_footer ); ?>

where $in_footer is false by default. If you set it as true then the script will be placed into the footer, but you will need to have wp_footer() in your theme.

You should check out the Codex for more info:

http://codex.wordpress.org/Function_Reference/wp_enqueue_script

Update:

Here is how it’s done in the plugin JavaScript to Footer to move all the javascript files from the header to the footer:

remove_action('wp_head', 'wp_print_scripts');
remove_action('wp_head', 'wp_print_head_scripts', 9);
remove_action('wp_head', 'wp_enqueue_scripts', 1);
add_action('wp_footer', 'wp_print_scripts', 5);
add_action('wp_footer', 'wp_enqueue_scripts', 5);
add_action('wp_footer', 'wp_print_head_scripts', 5);

See the plugin source:

http://plugins.svn.wordpress.org/footer-javascript/trunk/footer-javascript.php