I used the examples shown here and elsewhere, and it is really frustrating to see how many places this code example is messed up. Turns out the answer is simple, IE has special 'conditionals' like [if IE], but other browsers need comments to work with the 'conditionals'.
For example, since JQuery 2 doesn't work with IE8, you can do something like this
<!--[if IE ]> (following is only visible to IE)
<script src="./js/lib/jquery-1.6.1.min.js"></script>
<![endif]-->
<!--[if !IE]>--> (extra comment - only visible to non-IE)
<script src="./js/lib/jquery-2.1.1.min.js"></script>
<script src="./js/lib/jquery.mobile-1.4.5.min.js"></script>
<!--<![endif]-->
I have verified the above works in Firefox, Chrome, IE8, Dolphin mobile, and Chrome mobile. You can also specify version. For example, less than IE 9 would be: <!--[if lt IE 9 ]>
For a detailed explanation, check out http://www.sitepoint.com/web-foundations/internet-explorer-conditional-comments/