What do you want to do?
What you mention are valid options but it depends what you want to achieve. What are your needs for "finished" courses?
I run my own moodle, so here is what I do.
I keep the course available for students (meaning visible) for about 1 to 2 months, then I hide it. I let students know if that if they ever need to see something, that they can email me and I can turn the course back on for a little while.
I back up my entire moodle every night and keep a 7-day moving set of backups. About once every two months, I move one of these backups to a secondary drive, just for protection. I do not do any course-level backups.
With each major release of Moodle (2.0, 3.0) I make a complete backup of my production moodle, and begin a brand new installation of moodle. So right now, my production moodle started at Moodle 3.0.
I keep a running copy of my old moodles on my MAMP system (of course, on my Mac). This allows me to reference anything from history. So right now, I could go back to my very first Moodle course and see what students were in it, and what they did. (I also keep complete logs.) My old moodles tend to consume around 2GB of hard disk space.
I am always eager to hear suggestions to improve my system.
