The Flavor Bible is interesting (and so badly wants to be a web app). There are things it's amazing at; for instance, if you have one or two base ingredients, The Flavor Bible will generate thousands of plausible soup ideas. I don't find that it informs my cooking all that much though; the most important combinations are also very well-known.
Yep, foodpairing.com is a great tool for this. In the longer term I would prefer to not to need it at all, but for now foodpairing + a set of cooking patterns is what I am concentrating on.
Thanks for the book titles, added to the top of the reading list!
There's scientific analysis that can be done on flavor compounds in foods as well to find complementary flavors, foodpairing.com is working on this.