With the huge explosion of mobile devices and addition of HTML5/CSS3, there seems to be a shift towards "responsive" designs (i.e., adapting to smaller screen sizes) which seems to be achieved using CSS3's Media Queries.

My question is, given the current need of adapting to both desktop and mobile, is it common practice to actually organize two versions of your website (one for desktop and one for mobile)? Or is there just one version with different css files for targeting different devices and screens?

Handling just cross-browser (ie6, ff3, opera9, etc...) HTML4/5, CSS2/3 was already hard enough, but now we're expected to handle cross-device (phone, tablet, etc...) as well, so my assumption is company's would create a separate project for mobile and redirect based on the user agent, but this is just a guess.