The best resources available are:
- The Codex – Most of the functions and tools you’ll want to use are documented there, as well as examples and code snippets that you can use in your own system.
- PHPXref – There are a lot of different systems out there, I just linked to the first one I found. But remember that the in-line documentation for WordPress is pretty much amazing and, in many cases, will be all you’ll ever need.
- Justin Tadlock’s Blog – During the theme development presentation at WordCamp Portland, the presenter actually said his first step to learning a new technique or using a new tool was to see if Justin had written a tutorial on it.
Beyond those three references, I would also recommend that you take a very close look at the structure and composition of the TwentyTen theme that ships with WordPress. It’s written by the same team who writes core, so it’s your best bet for a “definitive” example of most things WordPress.
I’d also suggest you invest in one of the nicer theme frameworks available – my personal recommendation would be Genesis. If you’re using a framework for building your theme, most of the work is done for you. You’ll also have more tools at your disposal, and some of the frameworks are incredibly advanced in their design. Looking at how someone has already done something and deciding how you’d improve on it can be one of the easiest ways to learn.