Use remote computer without disturbing local user

Solution 1:

Perhaps the Sysinternals PsExec program would suit your needs?

http://technet.microsoft.com/en-us/sysinternals/bb897553.aspx

This allows you to launch console programs remotely and does not have a heavy installation/configuration process.

This will not allow you the rich user experience of a full fledged RDP connection, but I have found it perfect for short, simple tasks.

Solution 2:

You cannot login interactively two sessions simultaniously (wihtout hacking windows and violating your license agreement). If you are ok with that (considering system security and stability concerns + legal concerns), use the hack (jaoc's answer).

Depending you your programming chops (you are already writting scripts - I'd say you are almost there) you could create a windows service or a simple web application interface that would start your processes, and allow you to supply any necessary parameters through the web interface or an RPC call.

If there are no unique parameters for the scripts each time, just create a scheduled task to run your scripts.

+1 for PsExec. it could also do exactly what you need if you already have script or .exe you just need to run on the machine. If that meets your needs it would be even easier for you in the long run than the simultaneous session hack.