Google's mod_pagespeed plugin i.e. http://code.google.com/p/modpagespeed/ for apache will do auto-versioning for you. It's really slick.
It parses HTML on its way out of the webserver (works with PHP, rails, python, static HTML -- anything) and rewrites links to CSS, JS, image files so they include an id code. It serves up the files at the modified URLs with a very long cache control on them. When the files change, it automatically changes the URLs so the browser has to re-fetch them. It basically just works, without any changes to your code. It'll even minify your code on the way out too.