add them to $form['hidden']:
$form['hidden']['foo'] = 'bar';
the key is the name tag, and the value is the value tag, as per qa-theme-base.php:
function form_hidden($form)
{
if (!empty($form['hidden']))
foreach ($form['hidden'] as $name => $value)
$this->output('<INPUT TYPE="hidden" NAME="'.$name.'" VALUE="'.$value.'"/>');
}