I would agree that plugins should go in the plugins folder. I normally setup an instance of the resource autoloader during bootstrap using my app's custom namespace. E.g. say your app's namespace was 'Bob':
protected function _initAutoloader()
{
$autoloader = Zend_Loader_Autoloader::getInstance();
$resourceAutoloader = new Zend_Loader_Autoloader_Resource(array(
'basePath' => APPLICATION_PATH,
'namespace' => 'Bob',
'resourceTypes' => array(
'model' => array(
'path' => 'models/',
'namespace' => 'Model'
),
'form' => array(
'path' => 'forms/',
'namespace' => 'Form'
),
'plugin' => array(
'path' => 'plugins/',
'namespace' => 'Plugin'
),
'service' => array(
'path' => 'services/',
'namespace' => 'Service'
)
)
));
$autoloader->pushAutoloader($resourceAutoloader);
return $autoloader;
}
Add or remove resource types as required. You can then put your plugin in application/plugins/Whatever.php and it will be autoloaded as normal.