If using Lighttpd as your web server, add the following to Lighttpd's main config file:

url.rewrite-once = (
   "(.*\.(js|ico|gif|jpg|png|css|html|php))(\?v=.*)?$" => "$1",
   ".*\?(.*)$" => "/index.php?$1",
   "" => "/index.php"
)

Note: The "php" part in the first rule is to be able to load the javascript language file, which is actually a php file.

Make sure you have mod_rewrite enabled by putting the following somewhere above the previous block:
server.modules += ("mod_rewrite")