The JQuery update module gives you some trouble when you are working in a multisite environment.
Here's the .htaccess snippet i use to pull off the deception:
RewriteCond %{HTTP_HOST} example.com$ [NC,OR]
RewriteCond %{HTTP_HOST} justinhileman.info$ [NC]
RewriteRule ^misc.jquery.js$ sites/all/modules/jquery_update/jquery.js [L,QSA]
How to use your new superpowers:
1. Add the above snippet to your .htaccess file AFTER the RewriteBase directive but BEFORE the line that says
# Rewrite current-style URLs of the form 'index.php?q=x'.
2. Replace the example domains with any of your domain names.
3. Add a new condition for every site you want to use the jQuery update on.
4. Note that every RewriteCond line before the last one should end with [NC,OR], otherwise Apache will match the conditions with AND, i.e. nothing will ever match.
5. Make sure you have jQuery update module installed and enabled on every site you use the rewrite rule for. Otherwise Drupal could get a bit confused.
Also note that I assume your jQuery update module is located in sites/all/modules.
There will be an error in your status log. That's because, while every external visitor will see the new version handed to them by the fancy Apache rewrite, the jQuery update module is looking at the hard drive of your server and seeing the old core version. So feel free to ignore the error :)