We're currently developing a web-based course frontend for students and teachers in our uni (U. of Helsinki), which pulls some data from the student information system and some data from Moodle.
One of the planned features is showing notifications from Moodle courses on the "home page" of students.
An existing implementation that we know of is from University of Tampere, they have written a custom message output plugin that sends HTTP requests during the Moodle cronjob.
The downside of this plugin is that it needs patches in the lesson, assignment and quiz modules, among others. The reason for this is that the modules do not attach course identification data to the notifications (namely, course->id and course->idnumber).
From the web service API, we can poll notifications by user, but not per course (core_message_get_messages). Also, the get_messages function does not return course information.
So, I'm thinking, that we either have to give up on getting course level notifications from Moodle, or patch the core modules. Any other takes on this?