Command line RDP call CMD on target machine
Solution 1:
If you need to use RDP to access these machines, there are shells for mstsc.exe that allow command line auto-login and running a program upon connection. One that comes to mind is Remote Desktop Plus. You could use a batch script to log in to the given machines with the following syntax:
rdp /v:computer /u:username /p:password /start:"pathtoscript/script.bat"
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Solution 2:
Windows Remote Shell is what you want;
http://technet.microsoft.com/en-us/library/dd163506.aspx
Once setup, you can go WinRS -r:MYSERVER "cmd.exe"
which will run cmd.exe on the remote machine and bring you a remoted console session locally. Alternatively, you could just run any other command directly on the box instead.
Actually, if you are need to use RDP (and I wouldn't bother just to run a batch file if I could avoid it) you could run a shell (or any other command) without a 3rd party program. Just run mstsc.exe, choose an alternate shell and save the RDP file.
The key settings you need are looking for are;
full address:s:yourserver.domain.com:3389
alternate shell:s:c:\windows\system32\cmd.exe