Well thanks all - sort of makes sense too.As I understand it (and its a long time since I did biochem) it all comes down to the fact the cells in your body want to 'burn' a compound called ATP, so the "good" and "badness" of calories is effectively the difficulty with which your body can convert the raw calories you stick down your gullet into ATP.
If you are eating a whole load of sugary crap then that sugary crap is very easy to turn into ATP so you body will use it preferentially, and because you were evolved over millions of years/designed last tuesday to survive it'll even store some of it as glycogen and fat.
If on the other hand you eat a whole load of wax fruit by mistake (since calorie content is measured by burning in a bomb calorimeter it would have a high calorie content but your body wouldnt be able to use them at all) you body will preferentially burn its own stores of energy - ie fat.
So different calories consumed have different results.
So basically as far as dieting is concerned "good" calories are going to be hard to turn into ATP - protein and manky long chain carbohydrates (fibre) and bad is short chain, high energy stuff like sugar, alcohol and petrol.
Man work is boring today.