Remotely invoking shutdown on a Windows machine, as you're describing requires two-way communication between the host initiating the shutdown and the host being shut down. Authentication is "baked in" to the protocol, so you'll also have to get the host initiating the shutdown to authenticate properly.
A simple script to remotely invoke the shutdown on a remote non-domain-joined computer would be as follows:
net use \\x.x.x.x\ipc$ /user:administrator password
shutdown -s -t 10 -f -m \\x.x.x.x
met ise \\x.x.x.x\ipc$ /delete
Substitute in the IP address of the remote server for "x.x.x.x" and the local Administrator username and password on the remote server on the first net use line.
Relying on "seeing" computers in "My Network Places" doesn't, unfortunately, tell you too much about what kinds of traffic are permitted between machines.
I just sniffed such an exchange between a Windows Server 2003 machine and a Windows 2000 Server machine (which, funnily enough, is running an old 2003-era Cisco CallManager 3 installation for one of my Customers) and performed the shutdown using the script above (though I rebooted their server, rather than shutting it down-- the packet exchange is the same). I observed that TCP ports 139 and 445 were used to move the traffic. I'd guess that if I had only port 139 open it'd probably still work, but you'd have to try that to see.
If you want to use the name of the CallManager server, rather than the IP address, in the shutdown script then you'll need to have either NetBIOS or DNS-based name resolution working.
Edit:
That's not so much a "Windows problem" as a hardware power-management problem, typically. You may have the wrong HAL installed, or the BIOS power management support may be turned off.
You can try adding the REG_SZ value "PowerdownAfterShutdown" in "HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon" and setting it to "1" to see if it has an effect on the behavior.
Check the BIOS and be sure that power-management functionality is enabled.
This is a licensing problem; you are using the wrong release of Windows Server 2003.
Windows 2000 Advanced Server can only be upgrade to Windows Server 2003 Enterprise Edition, upgrading to the Standard one is not allowed.
Best Answer
Last time I did a migration, I used this guide to make sure I won't forget anything.
How to Migrate Windows server 2000 to Windows server 2003 Step By Step Tutorial
You can also check this :
Common Mistakes When Upgrading a Windows 2000 Domain To a Windows 2003 Domain