If we are talking about how to build story and characters, I cannot recommend enough this book:
http://www.amazon.co...e/dp/0312302762
Despite the title (its second half that is), it really is a book on how to make excellent fiction in general (not just in writing), and it applies to creating custom story-heavy modules as well. Basically, the author goes deep into what makes interesting stories (characters, worlds, anything) interesting, and then, based on that, he explains how to create an engaging story from scratch and how to keep developing it into perfection.
I've been working on my fantasy and sci-fi stories for as long as I remember, mostly in my head throughout daydreaming and, rarely, writing short novels. But it was a very chaotic experience, I didn't know the method, I just made everything up on the fly. This book gave me the definitive structure to use both when I am stuck, unable to come up with any ideas, and when I have too many ideas in my head and don't know which one to select. Also it made me appreciate good stories more, since now I know better how they are constructed and why they are as good as they are. '>