You can override many values or override subfunctions of the list object including the complete "where" part of the sql query. Example from web_domain_list.php:
$list = new list_action;
$list->SQLExtWhere = "type = 'vhost' AND parent_domain_id = '0'";
$list->SQLOrderBy = 'ORDER BY domain';
The list object is defined in lib/classes/listform_actions.inc.php, its a good place to get a overview of the existing functions. Basically you can override nearly every aspect of the list generation and query building in ispconfig.