To iterate by all application instances installed on current endpoint, use APSControllerProxy::listInstances() method, as follows:
<?php
...
foreach(\APS\ControllerProxy::listInstances() as $instanceId) {
$apsc = \APS\Request::getController($instanceId);
// do something wirh the instance, for example get all application resources:
$resList = $apsc->getResources();
...
}