If you have a look into the default format System.Web.Optimization.Scripts.DefaultTagFormat, you will find that you have something like:
<script src='{0}'></script>
So, the only thing you have to do is define a new format. You can do this using the "RenderFormat" method, like:
<%: System.Web.Optimization.Scripts.RenderFormat("<!--[if lt IE 9]><script src='{0}'></script><![endif]-->", "~/bundles/IE9js") %>