We are fairly new to Moodle, having made the switch gradually from Sakai in Jan 2012, then completeley on July 1, 2012. We have over 3000 students, 200+ Faculty, 500+ courses.
We still manage our users manully, and see no need to change. I have looked at using Active Directory authentication, but have not put it in place, since it would only benefit the faculty, ( students do not use AD ).
Faculty do have to add the students manually, which the faculty like, since it gives them control of who has access to the class. I experimented with cohorts at the begining, but so many students switch cohorts, it was impractical.
I have to say, I do not spend a lot of time on user management, I do not forsee any problems in the future manually managing them.