To really set WordPress loose as a CMS, we need a method to make Ajax calls and even to have pages that don't load the entire WordPress application (as calling wp-config does), but yet can give you whether user is logged in or not and give you the User's ID.
I have done this for my to-do list site that is built on WordPress authentication, but I fear that future upgrades will break my hack. I also use CodeIgniter's Active Record implementation for the DB layer. Works great, but not future proof.
Cheers!
Byron