What Knowledge Gaps Do Self-Taught Programmers Generally Have?

BeardedChimp writes "I, like many others here, have learned to program by myself. Starting at a young age and learning through fiddling I have taught myself C++, Java, python, PHP, etc., but what I want to know is what I haven't learned that is important when taught in a traditional computer science curriculum. I have a degree in physics, so I'm not averse to math. What books, websites, or resources would you recommend to fill in the gaps?"