Adding the following code in any PHP area in Drupal will give you settings values available client-side that you can use when writing JavaScript code.

Pass a key/value associative array to drupal_add_js() and give it type value of 'setting'. Note that I am using an array of arrays with the key of the first array as the name of the module. This is to namespace the settings. This will keep your settings from overriding others and others from overriding yours.

//PHP code in your module or in a PHP snippet anywhere on your site
 
$jquery_settings = array(
  'myModule' => array(
    'mySetting1' => 'myvalue1', 
    'mySetting2' => 'myvalue2' )
);
drupal_add_js($jquery_settings, 'setting');

Now, within your JavaScript you can access these settings that you defined server-side

/**
*  My JavaScript File
*/
alert(Drupal.settings.myModule.mySetting1);
// displays myvalue1