There are two methods to removing drupal.css from your theme in phptemplate.

The first cuts out the link from the $head variable. In page.tpl.php, replace your print $head

print str_replace('<style type="text/css" media="all">@import "misc/drupal.css";</style>', '', $head);

The other method requires overriding the stylesheet import themable function. Simply add this to your theme's template.php file:

function phptemplate_stylesheet_import($path, $media = 'all') {
  if ($path != base_path() .'misc/drupal.css') {
    return '<style type="text/css" media="'. $media .'">@import "'. $path .'";</style>';
  }
}

Replace the leading 'phptemplate' of above function with your theme's name if you are using this code in a plain PHP theme.