Hi,
I'm looking for management software for schools, that provides management for courses, students, registrations, classes, etc. Can any one name some free ones? I prefer Java/(j)Ruby but any good stuff will do. I'm not sure a CMS will fit my needs, since I will need some custom stuff like notifications and emitting grades/classifications.
You are looking for something called a Learning Management System, or LMS.
Moodle (PHP based) and Sakai (Java based) are highly regarded platforms, but are very different beasts. Moodle is more of a typical PHP CMS app, whereas Sakai is more like your typical J2EE enterprisey application.
Sakai is open source and free. It looks like it supports what your looking for.
Blackboard is a major commercial vendor.
Do not go with PeopleSoft (recently bought by Oracle). My university recently switched, but the UI is horrible, and not a single student or faculty or staff member I've talked to likes it. Even someone I know in the IT department distances himself from it as much as possible (working on other projects).
I would be quite surprised if Oracle is able to salvage any usable application from this.