There are between 10,000 and 11,000 organizations worldwide actively using CiviCRM *right now* to manage hundreds of millions of contacts, receive millions of contributions, register millions of people for events, send millions of e-mails - and many other uses. But, stuff happens.
You may have noticed recently that the count of organizations using CiviCRM in your CiviCRM Resources "dashlet" on your Dashboard has fluctuated. You might be seeing text like this - "Used by over 6,588 organizations". Unfortunately, we recently suffered a hardware failure on our stats server, which is where the dashlet gets the latest count. This is not the same server which hosts our website.
The statistics will soon be back to normal. Please see https://stats.civicrm.org for more updates. Sorry for the confusion, and thanks so much for your patience.