Heart rate monitors are wonderful things, but they don't seem to give a very good indication of the number of calories you've burned on a given ride. They tell you how much oxygen your muscles needed, but there are so many variables, that you really can't draw any conclusions about one from the other.
There's a thread in the Clyde forum
, here on Bike Forums, about how to burn as many calories as possible with your bike. The takeaway lesson seems to be that it's calories per hour, not calories per mile, that we should all be paying attention to. If you can hold a heart rate of 180 bpm for an hour, say climbing a mountain on your road bike, or if you can go the same distance in two hours, maybe with a rate of 90 bpm, this time on the flats, you'll have burned more calories on the second ride.
Of course pushing your heart is good for other reasons, and you want to (1) get your resting rate down low as well as (2) see your HR plummet almost immediately when you finish exercising. But if you're asking about calorie burning, the answer on that one seems to be time.