When copying the files of a Drupal install, do not forget to copy Drupal's .htaccess file. If you've had the vexing problem where a site you've just manipulated has clean URLs turned on but they suddenly don't work, this may well be the reason. It took me fixing this problem many times before I realized what was going on.
Scenario
You make a directory for a new site, cd to the new directory, and use drush to download Drupal.
% mkdir mynewsite
% cd mynewsite
% drush dl drupal