MacroFactor[1] is the way.
For anyone who doesn't want to follow a link, MacroFactor's killer feature is you input your daily weight and your food and it creates a smoothed estimate of your non-water gain and loss in order to be able to give you a pretty accurate estimate of total daily energy expenditure after a few weeks. That way, you not only track what you're eating, but you know exactly how much you should be eating as well, in a way that is the only way short of checking into a metabolic ward to know your own body's true energy usage. Any other system out there is just guessing based on sample averages from past studies of other people.