Let me explain the scenario I'm in. Currently my company has a desktop set up so clients can individually log in and test our data processing software. This is currently in a linux environment for ease of management.

What I'm looking to do is possibly set up a web app with will show the gui/output of the software while processing and keeping all the libraries server side. Similar to what would happen if you were to ssh -X into the machine and run the software on your display.

The software package is written in c++ and is a windows exe.

I've been searching around but havn't came up with anything promising. I'm wondering if anyone has any ideas or simple solutions for this before I start working on this app. Any input is appreciated.

Not going to happen.
Not only are you trying to run an executable on an operating system it wasn't created for but you're trying to run one from a web application which any well secured server would block from happening.

And then you're trying to capture the output of the executable (hopefully not some graphical user interface you're trying to be screenscraping, which would be even worse) and somehow show that (I suppose in real time) to a client via a web browser.

Not going to happen.

And that's got nothing to do with JSP, everything with it being a web application.