Your guide should be user-friendly. Spend some time thinking about how students and professors will navigate through your guide to find their individual courses before settling on an organizational scheme. Once you've chosen an organizational scheme, keep it consistent.
Before you chose an organizational scheme, consider how your students might approach locating their course page. I organize my courses by date because even if my students can't remember the course abbreviation and number or the professor's last name, they know what day it is (or the day the class was scheduled to visit).