The logo can be changed by placing the image file in your includes/templates/YOUR_TEMPLATE/images directory and then going to includes/languages/english and copy header.php to includes/languages/english/YOUR_TEMPLATE and than edit the new copy
Code:
// added defines for header alt and text
  define('HEADER_ALT_TEXT', 'Powered by Zen Cart :: The Art of E-Commerce');
  define('HEADER_SALES_TEXT', 'TagLine Here');
  define('HEADER_LOGO_WIDTH', '192px');
  define('HEADER_LOGO_HEIGHT', '64px');
  define('HEADER_LOGO_IMAGE', 'logo.gif');
you can use any file name or extension (jpg,gif,png) just change logo.gif to your logo filename