This is more like "Ancient History" Starter Guide on header.php ;)
http://wp.tutsplus.com/tutorials/theme-development/the-header-php-what-needs-to-go-in-it-and-what-doesnt/#comment-19170

wp_register_script and wp_register_styles are not recommended nor best practice guide, it should be wp_enqueue_script only e.g.

function my_custom_script() {
wp_enqueue_script( ‘custom-scripts’, get_template_directory_uri() . ‘/js/custom-scripts.js’, ‘jquery’, ’1.0′, false );
}
add_action( ‘wp_enqueue_scripts’, ‘my_custom_script’ );

and this doesn't need to be registered at all.

Another example: https://github.com/thethemefoundry/twentytwelve/blob/master/build/functions.php

Cheers,
Emil