This solution is written in PHP, but it should be easily adapted to other languages.

The original .htaccess regex can cause problems with files like json-1.3.js. The solution is to only rewrite if there are exactly 10 digits at the end. (Because 10 digits covers all timestamps from 9/9/2001 to 11/20/2286.)

First, we use the following rewrite rule in .htaccess:

RewriteEngine on
RewriteRule ^(.*)\.[\d]{10}\.(css|js)$ $1.$2 [L]

Now, we write the following PHP function:

/**
 *  Given a file, i.e. /css/base.css, replaces it with a string containing the
 *  file's mtime, i.e. /css/base.1221534296.css.
 *
 *  @param $file  The file to be loaded.  Must be an absolute path (i.e.
 *                starting with slash).
 */
function auto_version($file)
{
  if(strpos($file, '/') !== 0 || !file_exists($_SERVER['DOCUMENT_ROOT'] . $file))
    return $file;

  $mtime = filemtime($_SERVER['DOCUMENT_ROOT'] . $file);
  return preg_replace('{\\.([^./]+)$}', ".$mtime.\$1", $file);
}

Now, wherever you include your CSS, change it from this:

<link rel="stylesheet" href="/css/base.css" type="text/css" />

To this:

<link rel="stylesheet" href="<?php echo auto_version('/css/base.css'); ?>" type="text/css" />

This way, you never have to modify the link tag again, and the user will always see the latest CSS. The browser will be able to cache the CSS file, but when you make any changes to your CSS the browser will see this as a new URL, so it won't use the cached copy.

This can also work with images, favicons, and JavaScript. Basically anything that is not dynamically generated.

man curl:

   -H/--header <header>
          (HTTP)  Extra header to use when getting a web page. You may specify
          any number of extra headers. Note that if you should  add  a  custom
          header that has the same name as one of the internal ones curl would
          use, your externally set header will be used instead of the internal
          one.  This  allows  you  to make even trickier stuff than curl would
          normally do. You should not replace internally set  headers  without
          knowing  perfectly well what you're doing. Remove an internal header
          by giving a replacement without content on the  right  side  of  the
          colon, as in: -H "Host:".

          curl  will  make sure that each header you add/replace get sent with
          the proper end of line marker, you should thus not  add  that  as  a
          part  of the header content: do not add newlines or carriage returns
          they will only mess things up for you.

          See also the -A/--user-agent and -e/--referer options.

          This option can be used multiple times to add/replace/remove  multi-
          ple headers.

Example:

curl --header "X-MyHeader: 123" www.google.com

You can see the request that curl sent by adding the -v option.