There are many ways:

• Use ssh. This requires you to install an SSH server on the target machines.
• Use WMI. This requires you to have the appropriate permissions in your domain to launch processes remotely.
• Have a periodic job on the target machines fetch and run a Perl program that sits at a well-known location. To run a program on a machine, you put the appropriate script into the well-known location.
• If it's just to access files remotely, just have the machines export the relevant directories via SMB.
• Use Win32::GUI to automate the Windows Terminal Server Client and send mouse clicks to it.

I don't know Windows Server 2003, but I'm told that you can operate it through the text console, so I assume that the Microsoft documentation about Windows Server 2003 has information on how to do that. I would read the documentation to learn more about the environment.

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