Moodle allows a lot of flexibility with organizing courses. Plus you can re-organize to fit your needs. At LearnBPS (our 3.3 Moodle), we organized into three large categories. Of the three the Student Blended Learning is where the courses for school district is organized.
Bismarck organized the courses by subjects for the secondary (grades 6-12) courses. The reason for this was so that we could then organize subject-like standards and resources for those course in a central location for subject-like teachers. That way they could have a shared workspace to construct and create activities and resources.
The elementary is starting to use Moodle. Of course elementary teachers teach all content areas, so we are in a process to map out how we want to organize the elementary courses. That is what is powerful about Moodle is the flexibility users have when organizing their content...