Windows to Linux Migration - File Server Security?

Circuit Breaker asks: "I'm in the slow process of migrating my office from Windows to Linux. The servers have been Linux machines for quite a while now: Samba serves as PDC/BDC (not using Active Directory yet), and the Samba config is mirrored with rsync; all works well. No, it's time for the workstations, and all is NOT well. User lists are synchronized with NIS, which sort-of works, and will probably work better once we implement LDAP; but it seems that mounting of server directories can only effectively be done with NFS, which is a problem with security because some people really need local root. I've tried using NFS, CIFS and SSHFS, through pam_mount, automount, and independently, but it's not close to the usability of the Windows setup. It's either mounted per user, which requires a lot of work, or by root, in which case local root users bypass any remote permissions. How do you set up mounting directories that is easy to use like Windows -- everything automounted, but security settings are still respected for each user, even when local roots are involved?"