Thanks for the suggestion. The system is already mostly module-ized with a few glaring exceptions that need to be fixed.

My big problem is how do I let customers modify the modules themselves, without actually modifying the module? E.g. I'd like to some how give them the ability to, say, add company specific fields to the pre-existing User module and database, without actually modifying the User module source. I'm not sure how to handle the database.

This is the goal for me so future updates can be seamless, no matter how extensively customized their actual version of the application is.