Multiple installs with a single core system

Hi everyone,

Definitely a "Best Practice" question and I have absolutely no starting point so please feel free to make as many suggestions as possible.

I have a relatively successful web application built in Codeigniter. Each customer gets their own subdomain which has a basic version of Codeigniter. Each class within codeigniter then extends a class from a core folder I've created. The core folder has a "site wide" version of the controllers, models and views. This allows me to keep the main system specific code in one place as well override the classes when a customer asks for something specific to them.

I've always thought of it as a bit clunky but it got the job done at the time.

I'm about to start a new project which will potentially have multiple customers using it again, ideally on their own sub domain. I've thought about building it as a single application but prefer to have separate domains/databases as much for security of data as well as anything else.

With that in mind, does anyone have any suggestions as the best way to move forward with separate subdomain/database installs of the same code but easily updatable.