You'd need to check your documentation. Typically if you are launching an application from command line, you'll need to provide it with all of the arguments it requires. PHP would be limited to trying to interact with the process itself (using proc family may be able to help with that). If there is a way for it to be done from the command line calls, than sure you can do that. Maximum and fullscreen options for video players can *likely* be performed at the command line call. If they have it in, you can try launching the executable with the /? on it which typically brings up the help menu in windows to show you what arguments it will accept.
Java can make use of the Robot class which allows you to click on the screen. I've never tried to set up a client / server application which uses the robot before, but I'd presume you can issue commands remotely that would interact with the Robot. Positioning is where the pain will be.
Is there any reason why you don't simply use remote desktop to control it instead? Sounds like it would be a lot easier than writing something to do it.