+1 for using Browserify. We use it here at diy.org and love it. The best introduction and reasoning behind Browserify can be found in the Browserify Handbook. Topics like CommonJS & AMD solutions, build pipelines and testing are covered there.
The main reason Browserify works so well is it transparently works w/ NPM. As long as a module can be required it can be Browserified (though not all modules are made to work in the browser).
Basics:
npm install jquery-browserify
main.js
var $ = require('jquery-browserify');
$("img[attr$='png']").hide();
Then run:
browserify main.js > bundle.js
Then include bundle.js in your HTML doc and the code in main.js will execute.