app.js

var express = require('express');
var app = express();

// ...

module.exports = app;

server.js

var app = require('./app');

app.set('port', process.env.PORT || 3000);

app.listen(app.get('port'), function() {
  console.log('Express server listening on port ' + app.get('port'));
});

Setting up express.js separating app bootstrapping and server startup.