By default when you use wp_enqueue_script the script is inserted into the <head> section. This is usually set in functions.php.
The argument also has a footer option called $in_footer, if you set this to true, the scripts will instead be added to the footer section. In TwentyTwelve there are several calls to wp_enqueue_script with footer set to true.
For example:
wp_enqueue_script(
'twentytwelve-navigation',
get_template_directory_uri() . '/js/navigation.js',
array(),
'1.0',
true
);
To remove the footer calls you can wp_dequeue_script it, then requeue it for the header or just add false for the 5th parameter.
http://codex.wordpress.org/Function_Reference/wp_enqueue_script
Ref:
wp_enqueue_script(
$handle
,$src
,$deps
,$ver
,$in_footer //this
);