I'd like to launch CPU and GPU intensive process on some machines, but these processes must not interfere with user's tasks. So I need to limit or at least detect GPU usage by my processes. These processes are closed-source, so I can't watch GPU usage from inside.
The answer to your subject line question is: yes (On Windows Vista and up), use Process Explorer from Microsoft to monitor per process GPU usage. nvidia's parallel nsight can do this also. Now, the body of your question sounds like you want to do this remotely. Unfortunately I'm not aware of a way to do this remotely. Still, hopefully this will be of some use to you.
edit to add: If you fire up Process Explorer I don't think it shows the GPU stats by default, to get them right click on the list of columns and add them.