di.js

// you can omit DI for _light_ dependencies
var async = require('async');
 
module.exports.inject = function( dependencies ){
  
  // no direct require of _heavy_ dependencies
  var mysql = dependencies.mysql;
  var redis = dependencies.redis;
  
  // do whatever
  
  return // some presistence object
  
}

Each module in the application follows the same design.

Your server.js file can assemble the ensemble with:

var di = {}
di.mysql = require('./mysql').inject( di );
di.redis = require('./redis').inject( di );
di.app   = require('./app').inject( di );

// do something with di.app