Media Queries was not supported by Microsoft until IE9 in Feb 2011. There are still a large percentage of users who do not have the proper browsers to support Media Queries. To make things even worse, most of the Media Query sites are not written in a way to show a reasonable default page for older browsers.
Check out the page "Is this the same as Media Queries" on either site.
According to the latest browser stats, about 18% of all visitors to your site will have IE8 or lower. What will your site look like to about one customer in 5?
The advantage to this JS version is that it will work on just about every browser and it contains an exact default choice for the few browsers that do not support JS.
The script allows you to start working with alternate style sheet design now while supporting every visitor to your site. Most of the MQ sites are showing garbage to 18% of their visitors.
As the page I mentioned states, MQ is the way of the future, but due to MicroSoft's lack of early support, it's time is not now unless you only want to support the higher tech customers and are willing to turn away the rest.