Pro Sites and Security, Backups Etc

When setting up Pro Sites, what security measures (plugins, settings, backups etc) are currently recommended for the primary multisite install? Also, can end users add plugins to secure and back up their own sites?

What (if any) security measures were taken for a site like Edublogs?

Thanks. I'm relatively new to this and just want to keep things in line as best as I can from the start.