The official Codex is the best place to start. One other thing you can do is look through the Default theme that comes with Wordpress and take a look at the code to see some of the more popular wordpress tags in use and you'll get a good idea on how to start your own theme. I've built around 40 custom wordpress themes for high end brands now and I started off a few years ago by modifying the default theme. It's a great way to see how Wordpress works.
Remember, Wordpress is just the CMS, 50% of the site. The other half is the theme and how to use the information in the CMS. So if you're building a website in Wordpress the first thing you need to do is have the structure of the site cemented first before even installing Wordpress. Once you know your site structure and how you want the site to work you can start structuring your content in Wordpress... refining it as you go along.
Wordpress is a great blogging platform, but with a little work it becomes one of the most widely used free CMS systems out there and for good reason. I love it.
If you need a hand with anything I'm more than happy to offer advice and pointers.