[eluser]BrianDHall[/eluser]
After a little thinking, it might be best to do this by extending Controller with a MY_controller. In the MY_controller you build all your stuff that is common to the whole intranet, such as a login/auth system, perhaps basic page template concept (like every page will have header, footer, navigation, content, etc) etc.
Then you can build individual controllers for each micro-site or department to over-ride only the things they want differently.
So if HR wants special functions just for them, easy - just pop open the HR controller and add to your hearts content. If there is a bug or feature that needs addressed for the company as a whole, just pop open your MY_controller and fix/add any way you like and instantly all sites will benefit from your improvements.
For URL you can either use sub-directories or sub-domains, as the routes file makes it pretty easy - hopefully you will have access to .htaccess url rewriting, as this makes things just cleaner looking and gives you a little more leeway in how you rig URLs to work.
This I think would be the best combination of flexibility and code reuse, and if some crazy department wants to just be totally crazily different than all the others - no problem!
You'll just want to organize your views sensibly so it is easy to see what view is shared amongst most/all sites, and which ones are department specific. You can just use folders for that, CI doesn't mind.
EDIT: As for Models, you can just use them normally or any way you want. I can't imagine any reason you couldn't use one Users table/model login system with a department field to restrict functions by department or position, etc.
In theory if some new department wants a basic site you could throw it together in a few minutes with minimal copy/pasting - they'll just get a site like you designed your basic template. As they want changes you just over-ride as you go, extending and modifying without fear of screwing up some other department site.
