Weighting Javascript in .info files Drupal 7 adds a new 'weight' option to drupal_add_js so that you can control the order in which Javascript files are added to the page. Is there any way to do this when adding Javascript in .info files?
Despite its instructions to not use it for adding JS to every page, hook_init() will allow you to add JS in an more sophisticated way with drupal_add_js().

That said, it is rare that a JS file must be loaded on EVERY page, so there is likely more optimization you can do. Also see the FAPI property #attached for adding JS to a form.