You're unfortunately going to run into a problem pretty quick because, technically speaking, a universal language is impossible. Systems are going to have different architecture, different languages available, and different storage means. I believe what you intend (correct me if I'm wrong) is a "widespread" protocol. One way or another, you're going to have to drill down based on your personal use-case.
For a widespread example, you could keep a set of JavaScript files with functions server-side, and refer a web client to the one they need to run it by loading a javascript file during some event. Pass the location of the file and the function name, load it using the link above, then call the JavaScript function by name to run it. I could see this being an admitedly somewhat roundabout solution. This also may work in Java due to its built in JavaScript engine, although I haven't tested it.
Beyond that, I am unaware of anything particularly widespread. Most applications limit what they accept as instructions quite strictly to prevent security breaches (Imagine a SQL Injection that can run free on a client's machine). In fact, JavaScript limits itself quite severely, perhaps most notably in regards to local file reading.
Hopefully this helps with your ideas. Let me know in a comment if you have any questions/issues about what I've said.