browser.html

<script src="mootools.js"></script>
<script>

Moo.apply(this); // For non-strict browsers
Moo.apply(window); // For strict browsers

</script>

commonjs_app.js

// CommonJS
var Moo = require('mootools');

Moo.apply(this); // For most CommonJS implementations

// For strict CommonJS implementations
Moo.apply({
	String:String
});
var Class = Moo.Class;

MooTools.js

var Moo = function(){
	var context = this;

	var Class = this.Class = function(){};
	
	this.String.prototype.foo = function(){ return "foo'd"; };

	context.String.prototype.bar = function(){ return "bar'd"; };
	
};

exports.Array = Array;
exports.String = String;
// etc…

exports.apply = function(context, args){
	MooTools.apply(context);
	return context
};

exports.apply(MooTools);