Here's a script to change the server comment on an NT/2000 system:

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; This file lives at www.jesseweb.com
;----------------------------------------

$SCOMMENT = "ENTER YOUR SERVER COMMENT HERE"
$TEMP = WRITEVALUE("HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\LanmanServer\Parameters","srvcomment","$SCOMMENT","REG_SZ")
$TEMP = WRITEVALUE("HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\Services\LanmanServer\Parameters","srvcomment","$SCOMMENT","REG_SZ")
$TEMP = WRITEVALUE("HKEY_LOCAL_MACHINE\SYSTEM\ControlSet002\Services\LanmanServer\Parameters","srvcomment","$SCOMMENT","REG_SZ")

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TIP: You could also SHELL out and use NET CONFIG SERVER /SRVCOMMENT: WHATEVER