According to the Wordpress documentation, you should use wp_localize_script()
in your functions.php file. This will create a Javascript Object in the header, which will be available to your scripts at runtime.
See Codex
Example:
<?php wp_localize_script('mylib', 'WPURLS', array( 'siteurl' => get_option('siteurl') )); ?>
To access this variable within in Javascript, you would simply do:
<script type="text/javascript">
var url = WPURLS.siteurl;
</script>