I recently had this error occur on one of my Drupal multi-site installations. If you're here, you're having this problem, too.
The likely problem
If your site isn't uber-high traffic and you're seeing this message, it's very likely related to the Update Status module.
The solution
Disable the Update Status module, especially if this is a multi-site installation. You may also increase the wait_timeout setting, if you have permission to do this on your host.
Why does this happen?