Pawel,
Another idea is to create your own TCP interface in LabVIEW. If you have multiple licenses, you can use a second copy of LabVIEW, or if you don't, you can create an executable if you have the Application Builder. Your remote application will listen for TCP messages and do what it needs to do and send back the results. Your client program (on your machine that you are sitting at), can have a choice of command to run and send those to the remote application.
Another method would be to use remote panels with LabVIEW 6.1 and have your remote application act as a remote panel server. In this case, you could just bring up the panel of the remote application and run it as if it were connected to your machine. There are some limitations of using things this way
(like saving files would have to be done only on the remote machine), but this might work for you as well.
Randy Hoskin
Applications Engineer
National Instruments
http://www.ni.com/ask