Recently I came across a new book on Amazon "Far Inside The Arduino" by Tom Almy. This is one of the best book I have read on the topic. The book reads more like an in-depth article than long drawn out book. It's not for the casual Arduino programmer. Rather, it is for the Arduino power user wannabe. It has opened up my knowledge of Arduino boards a great deal.
If you are wanting to take your Arduino knowledge to the next level, this book is a must have. Shortly, after starting on this book, you learn how to cut the size of your programs by at least a factor of two and increase the I/O speed. You learn how to take advantage of interrupt service routines. Using that knowledge, you learn to use them to create state machines. S/W state machines are a big part of using microcontrollers to the best advantage. You learn timers and how to take advantage of the Watchdog Timer. You learn how to use the Serial Peripheral Interface (SPI), the Two-Wire Interface (TWI), controlling multiple stepper motors, and more.