If you really want to use group policy, your best bet is a Windows
2003 AD server. If at all possible you'll want to have at least two AD
servers for redundancy, fail over, etc. If you're looking into it at
this point and you're going to do any sort of licensing with Microsoft
you'll want to look into Software Assurance. Group Policy improves
with every iteration of the Windows Server OS, and 2008 is looking
really good. It sounds like you're looking at a new AD implementation?
If so, you'll want to go with native mode. Native mode means that all
domain controllers must be at the same version of Windows. Mixed mode
should be used for transitioning versions.

As for integrating Samba and Linux, the answer is Kerberos and Samba.
Samba knows how to participate in an Active Directory domain as a
Member Server. With winbind it can authenticate AD users. There's even
a PAM winbind module.

You can also setup authentication via Kerberos if you want to use
Kerberos aware services on your Linux computers. I haven't tried this
in earnest, but to get this all working I imaging you'll become
familiar with the ADSI Edit and setspn Windows tools.

Samba as a Domain controller emulates at NT4 style domain, so you
won't have access to anything group policy.

I'm not aware of any real alternatives to Windows Servers + AD. Novell
+ Zen maybe, I've got some Novell experience but it's on old versions.
When you're looking at managing Windows clients, Active Directory is
the right tool for the job.

-- 
Andrew S. Zbikowski | http://andy.zibnet.us
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