Conditional comments do not work within stylesheets. Instead, you can use conditional comments in your HTML to apply different CSS classes or IDs to elements that you can then target with CSS.
For instance:
<!--[if IE]>
<div id="wrapper" class="ie">
<![endif]-->
<!--[if !IE]>
<div id="wrapper">
<![endif]-->
Also, there are tools such as Modernizr that do feature detection in a very similar way (by adding classes to the <html> element). You can use it to progressively enhance your design/script for newer browsers while still supporting older browsers.