Nginx doesn't run the app. It is a webserver and it acts as a proxy in this case. The apps are run on a non-standard port and Nginx than relays then to port 80 on the correct domains.
Selecting the port to run on, is up to the app itself. Are these apps you've written or just things you've installed? Usually, you can set the port as an environment variable. So, you'd start your app with something like:
PORT= 4000 forever start --sourceDir /path/to/your/node/app main.js
That assumes that the app does something like the bellow. This is from the template created using express-generator, so it is fairly universal:
#!/usr/bin/env node
var debug = require('debug')('my-application');
var app = require('../app');
app.set('port', process.env.PORT || 3000);
var server = app.listen(app.get('port'), function() {
debug('Express server listening on port ' + server.address().port);
});
That defaults to using port 3000 unless the environment variable is set.