With CodeIgniter already offering a superb way of structuring your applications, some you just feel that you need to take things one step further to give your application that higher level of clarity, i.e. breaking your applications into modules.

While waiting for a future version of CodeIgniter to natively include modules, you could look at 3 extensions that currently allow you to spilt your application into modules.  These are Matchbox, HMVC and Modular Separation.

Out of the 3, I found that Matchbox was the closest at keeping compatibility with the CodeIgniter framework and at the moment, that is the one that I currently use for all my applications.  I believe HMVC and Modular Separation are PHP5 only so that should suit those that just wish to code in PHP5 only.

If you are interested in finding out a bit more about Matchbox, HMVC or Modular Separation, be sure to visit the CodeIgniter forums.