I think you can do it with drupal_add_js(); it seems that the scope key option is your friend!
It's worth looking at using this module here to manage that for you https://drupal.org/project/advagg
I did this: enabled AdvAgg Modifier, Advanced CSS/JS Aggregation. Then I visited settings page
where I checked options:
Enable preprocess on all JS,
Move all inline scripts to the bottom of the execution order,
Move JS to the footer - All.
And now i have all JS in the bottom (as google recommends), without need to chane html.tpl.php