Jesse Schell is the founder of Schell Games and is an instructor at the Entertainment Technology Center at Carnegie Mellon University. These cards help you look at game design though various perspectives. There is also a free version you can get from the apple app store.
Game Design Workshop: A Playcentric Approach to Creating Innovative Games, Third Edition3rd Edition Tracy Fullerton directs the Game Innovation Lab at The University of Southern California. This book clearly explains each aspect of game design and closely follows the Game Design Tool Kit. You can find the 1st & 2nd editions of this book for less than $15 and they aren't much different than the current edition.
Game Design the Research Paper for the 20th Century is a presentation I did at KySTE and couple of years ago. It has some examples of a Game Flow chart and Prototyping.