You just need to add this snippet of code to your package.json:
"scripts": {
    "start": "node app.js"
}
You can add numerous commands that run at various times in the lifecycle of your package. For more details you can take a look at this link where it has all the specification. 
By default the server expects to find a file server.js at the root of the project, as in your case the file you need to run is the app.js you need to specify it.
Below an example of a package.json simple that will serve p/ you.
{
    "name": "[NOME DA SUA APLICAÇÃO]",
    "version": "[VERSÃO]",
    "private": true,
    "scripts": {
        "start": "node app.js"
    },
    "dependencies": {
        "express": "~3.4.8"
    }
}
If your application is still working locally and not on your server, it is likely that the port you are reporting is not the one specified by the server. For example I use as a server the Appfog, and the port to be used by the application is informed via an environment variable process.env.VCAP_APP_PORT.
In my application it is more or less like this:
app.set("port", process.env.VCAP_APP_PORT || 3000);
...
http.createServer(app).listen(app.get("port"));