Print in head of index file (or in php include in header tags)
Any js file can use variables defined in same scope level above it, even if in other files.
http://www.w3schools.com/js/js_scope.asp
Common form is to, inside the tag and at before any other calls, to define all 'global' js variables.
Printing php into a js file is discouraged highly for a few reasons, even though i have heard its possible, but just use a php include if you need it in multiple places:
<html>
<?php
// include any shared content, in this case i include entire <head> section
include('header.php');
?>
<body>
So if you have something like this at top of your php index file, or in an include you place there:
<script>
var baseUrl = "<?php echo $GLOBALS['domain_name']; ?>";
</script>
Then that can be used as a standard variable anywhere after that point.
Side Note: using object wrapper
As a side note, you could wrap it in an object and pass that object through to other files, such as:
var AppData = {};
AppData.domain_name = "<?php echo $GLOBALS['domain_name']; ?>";
AppData.googleTrackerUID = "<?php echo $GLOBALS['gtrackerid']; ?>";
AppData.whatever = true;
fnct_from_earlier_point_or_elsewhere(AppData);
Thats only really of use if you think you may need to pass any other settings through, or just want to build for that possibility (especially if optional param, as easy to make reusable function that handles if an index doesnt exist)
I prefer the object approach, but dont overcomplicate if not needed.
EDIT
As @Amadan commented, it would even be easier to create the $AppData array/object in php then just call this:
var AppData = <?php echo json_encode($AppData); ?>;
Also, regarding someone posting to omit the 'var' keyword, its usually bad form as var doesnt stop it being global, and some issues with certain browsers (IE)
javascript var or not var, what's the difference?