[eluser]Colin Williams[/eluser]
Depends a lot on the specific architecture of your application. There is a Modular Extensions contributed library that allows for a different directory structure for MVC, meant to be more like self-contained modules. But it's not exactly a plug-and-play module system for any app.
CI doesn't really have a standard for this because it's best left to the application developers to decide how they want to allow for their apps to be extended/modularized. Lately I've been using a hooks-like system, whereby plugins/modules react to events and actions that happen in the app, like say when a blog post is loaded from the db, plugins can act on the returned result before it reaches the controller and ultimately view. Works well because the core blogging system doesn't need to know what plugins are installed, it just does its thing and invokes usable hook points.
