re: Use the backup.php script in moodlecode/admin/cli/. that script takes two parameters ... course ID and the destination for the backups.
Thanks for the tip, I'll keep it in mind. I already have a rough idea of the numbers of large backups and total backups, about 20% are 100-500mb the rest of the 500 courses are under 100mb. I don't anticipate the large courses causing the backups to crap out the server (although I am trying to convince people to reduce the size) but the sheer number will likely run a long time (wild guess 4-12hr).
I don't think our server could handle it during the regular business hours without impacting performance, which we've noticed when manually doing a big course now and then throughout the day. We are considering starting a backup at 10pm and praying it ends by 9am, otherwise we'ld need to end this process if regular users are negatively impacted (disable automated backups and kill the process in windows server and hope that stops the backup?)