If you can boot clients to Windows NT, 9x, 2000, or XP but do not want to have particular applications running on the workstations for some reason, a Terminal Server is your answer. Consider loading the terminal client to give the users access to these applications on the server in full interactive Win32 sessions.
You can, for example, put all your 9x clients into a workgroup and not connect them to any domain. They can load without requiring authentication, obtain an IP address from a DHCP server, and then load the Terminal Server client in full-screen mode. The user does not even see the old Windows 9x desktop, and the first logon screen is the Windows Server 2003 Terminal Server session at the server.
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