I wrote a review for Joseph Thibault's Moodle News on extension development for Moodle. The book is quite good and I think an essential resource for anyone wanting to develop in Moodle. The book focuses on plugin development, but it will also give you an overview of the architecture, api and best practices.
I wish I had this book about 3 years ago when I first started fooling around in the code base! At any rate, you can read the review on Moodle News at http://www.moodlenews.com/2010/moodle-1-9-extension-development-review-by-bseanvt/
There is also an interesting discussion underway about the 'bloat' in the Moodle code at http://www.moodlenews.com/2010/opinion-1000000-lines-of-code/
Just finishing up brewing up some fresh ground comments...