I've been developing games independently now for several years. Easily the most difficult part is the design. Merely implementing the game-- if only that was my biggest challenge!
- The Art of Game Design by Jesse Schell: http://amzn.to/zFOiEk
It's pretty comprehensive, but I found it a bit "heads in the cloud" and not very hands on. The lenses give you some hands-on approach if you apply them though. If you are looking for a book with very specific "how-to-do-this-or-that" then it may not be your thing.
I like to pair this book with David Perry on Game Design: http://amzn.to/ytXF7G
That monster tomb is all hands-on and You can use it more like a cheatsheet:"OK I need a villain. Let me turn to the 'villain archetypes' section and pick one at random. OK he needs a weapon. Let me turn to the 'rifles' section and pick one at random" and so on.
I also really liked "Level Up!: The Guide to Great Video Game Design" by Scott Rogers: http://amzn.to/xuVjWU
It is the book I recommend to budding game developers because it is sort of like "Art of Game Design" lite. It covers most of the same topics but don't go into such an intellectual depth which is a GOOD thing for people just wrapping their heads around what game design is. Once they finish that, I move them to Schell's book.
Some other great literature on games that also discuss flow can be found in Jesse Schell's book (http://www.amazon.com/Art-Game-Design-book-lenses/dp/0123694...) or in Steve Swink's book (http://www.amazon.com/Game-Feel-Designers-Sensation-Kaufmann...).
(edit: no coffee yet)
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