Hello,
I starting working with WordPress as a CMS, now that the V3 makes it way easier to manage taxonomies and custom post types. My work is mostly focused on developping plugins and themes.
My biggest plugin does some admin stuff (add admin menu items and the related pages and features), but also does some importing and exporting, and hooks some of the base post processing treatments ("when a new post is created").
My biggest theme is pretty small, and all it does is display custom posts in a custom way.
After a few weeks of work, I have several thousands of LoC, and it's getting harder and harder to dig into it. Which leads me to the following question : How do you organize your WP plugins code ? And what about your WP themes code ?