Drupal have a javascript array for save settings and variables, take a look here:
http://api.drupal.org/api/drupal/includes--common.inc/function/drupal_add_js/6
Check the "settings" option in that page.
A example could be:
$my_module_variables = array(
"url" => "http://google.com",
"name" => "this is a variable"
);
drupal_add_js(array("my_module_vars" => $my_module_variables),'settings'settings');
And for use it in your javascript files you can do:
console.log(drupal.settings.my_module_vars.url);
//will print http://google.com
console.log(drupal.settings.my_module_vars.name);
//will print "this is a variable"
In this way you can set javascript vars without need print javascript code, only using a php array.