Your second line has the opening comment delimiter in the wrong place:
<!--[if gte IE 9]><!-->
Notice from the syntax highlighting here that it now highlights correctly as a comment.
The rest of the markup that follows will highlight correctly as well, since the <!-->
is now seen as <!
followed by -->
, rather than <!--
followed by >
as it would have been in your invalid markup:
<link rel="stylesheet" href="Scripts/styleMain.css" media="all" type="text/css" />
<!--[if gte IE 9]><!-->
<link rel="stylesheet" href="Scripts/styleMob.css" media="screen and (max-width:500px)" type="text/css" />
<link rel="stylesheet" href="Scripts/styleDes.css" media="screen and (min-width:501px)" type="text/css" />
<!--<![endif]-->
<!--[if lt IE 9]>
<link rel="stylesheet" href="styleDes.css" type="text/css" />
<![endif]-->
The bits of your code that don't highlight as comments will be how IE9 and later as well as other browsers will see your markup. Older IEs will just see your first and last <link>
elements.