You need a require.register function in the scope where you add the wrapped files. It's recommended to use commonjs-require for this purpose.

gulpfile.js

var commonjsWrapper = require('gulp-commonjs-wrapper');

gulp.src('src/**/*.{js,coffee}')
.pipe(commonjsWrapper())
.pipe(gulp.dest('build/'))

its compile from:

src/sub/Cat.js

module.exports = function(){
	alert('cat');
};

src/Main.coffee

Cat = require 'sub/Cat'

module.exports = ->
	Cat()	

to:

build/sub/Cat.js

require.register('sub/Cat', function (exports, require, module) {
	module.exports = function(){
		alert('cat');
	};
});

build/Main.coffee

require.register 'Main', (exports, require, module)->
	Cat = require 'sub/Cat'

	module.exports = ->
		Cat()