User Subdomains with only one CI core

[eluser]Nick_MyShuitings[/eluser]
There really are too ways you can work it. I'll bring up the file structure since the reference bretticus sent (I have implemented in my toolbox stack) deals more with db. if you check over the file structure of index.php of the application folder, you'll quickly realize that you can move it wherever you want in relation to the system folder and even the rest of the application folder (although I prefer to keep it inside the application folder for obvious organizational reasons). You will also see that system is in no way dependent on application, and thus can support infinite applications.

My personal preference is the following:
system
webroot
-application1
--index.php
-application2
--index.php

Where system is not even web accessible and multiple application folders are running off the same core system and contrib libraries.