I'm a LAMP user trying to run a Windows photo processing app remotely from a web interface. I basically just need to be able to pipe the file upload to the interface. Is there a way to do this remotely by just sending the file (instead of having to use the full Windows GUI)?
Not generically. There is no uniform Pipe Files to Windows GUI Elements method in Windows.
I'm afraid you're at the mercy of the photo processing application and whatever interfaces the developers of that program decided to put in. That would be the best solution.
There are some extremely hacky and fragile methods of faking it, but that's the chewing-gum and twine method.