It turns out that the Update module that comes with Drupal runs some pretty hefty queries. While trying to debug a crazy mysql error we were seeing on one of the sites I work on (http://drupal.org/node/361563) it occured to me that there is no reason why we should have the update module enabled on our production site at all.

Turning it off on production (while leaving it on on staging) gave the site a nice litte pick-me-up especially after clearing the cache.