Mootools, downloaded from github, comes with packaged with a utility called Packager. I wrote an article on using this tool. It is great for packaging your code prior to deployment but it doesn't work for dynamic loading in the client. Aaron Newton created a useful tool called Depender that dynamically builds a script for your page. His solution requires running Django on your server. This isn't always possible with shared hosting.
This is very useful during development. Because RequireJS also comes with a build tool, you can use the plugin and configuration to build a production ready script. Check out the project page for more information.