The documentation regarding notifications (http://doc.ez.no/eZ-Publish/Technical-manual/4.6/Features/Notifications/Using-the-admin-interface) is not clear enough on what cronjobs should be run in this context.
Cronjob.ini specifies by default that the cronjob required to execute notifications is "notification.php", and includes it under the "frequent" cronjob part, so it should be mentioned that in order to execute subtree notifications, the following command should be issued:
php runcronjobs.php frequent
Please note that the documentation on "Configuring cronjobs" (http://doc.ez.no/eZ-Publish/Technical-manual/4.6/Features/Cronjobs/Configuring-cronjobs) is already good, as far as notifications are concerned. But it makes sense to enhance documentation so that this information is also available on the "notifications" section.