How do I apply cufon.js only for Internet Explorer, in template.php?
You can't apply JS only to one browser using Drupal functions. What you can do is:


CSS workaround:


apply CSS only to IE
assign some style that will not be visible, but also will not be present in non-IE, like white 1px border on white background
use css() jQuery method to test if element has property you expect it to have in IE, and if true, execute your code.

JavaScript way:
Use jQuery Browser Plugin or similar solution to identify browser inside your js file. Execute your code if it's the browser you need it executed in.