Seems to me that finding the most comfortable and efficient handle bar height (and stem length) are so dependent on and individual's flexibility and morphology
that one can't depend on "rules of thumb". Consider going down to your LBS and asking them to look at your position on the bike and help you fine tune your fit.

That being said, a lot of folks that I see tend to have their bars set 2 to 3 inches lower than the top of their saddles.

Good luck!