An example webpack config that I'm not sure handles external dependencies correctly.

webpack.config.js

var path = require('path');
module.exports = {
  entry: {
    module1: './static/js/module1.js',
    module2: './static/jsx/module2.jsx',

    module3: [
      './static/vendor/drop/drop.min.js',
      './static/vendor/jquery-timepicker-jt/jquery.timepicker.js',
      './static/jsx/module3.jsx',
    ],

    module4: [
      './static/vendor/jquery-ui/ui/minified/jquery-ui.min.js',
      './static/vendor/fancybox/source/jquery.fancybox.js',
      './static/vendor/fancybox/source/helpers/jquery.fancybox-thumbs.js',
      './static/vendor/bootstrap3/dist/js/bootstrap.min.js',
      './static/jsx/module4.jsx',
    ],
  },
  module: {
    loaders: [
      { test: /\.jsx$/, loader: 'jsx-loader' }
    ]
  },
  output: {
    path: path.join(__dirname, 'static/dist/js'),
    filename: '[name].bundle.js'
  }
};