For scritps and using the wp_register_script() function, you can define the dependeny of jQuery in the $deps argument, which is documented as:
$deps: Array of the handles of all the registered scripts that this script
depends on, that is, the scripts that must be loaded before this
script. These scripts will automatically be enqueued when this script
is enqueued with wp_enqueue_script(). Set false if there are no
dependencies. Default: array()
http://codex.wordpress.org/Function_Reference/wp_register_script
Example:
wp_enqueue_script('custom-script', get_stylesheet_directory_uri() . '/js/my-jquery-custom.min.js', array('jquery'), '1.0', true);