Calories in vs calories out is not an absolute science. For example, if today I ate nothing, ran 5 miles, did weight lifts, etc I would probably burn more than 3000 calories. Will I lose any weight today? No. You body doesn't work like that. It isn't going to suddenly start using all the resources within - hence losing weight - when it doesn't have a short run supply of food. If it was this simple, our cave brothers and sisters would have died and probably half of our population wouldn't exist. The fact remains, our ancestors probably didn't find food as quickly as one can today; your body begins to utilize the food already given. History proven one thing, most people die from lack of water than lack of food; that is why the connection between food and weight has never been fully established until recent times.
After much thought, I figured weight management has more to do with your diet over time, and not your diet in a finite timeframe. For example, if I were to eat only donuts everyday, I would indeed lose weight due to the lack of calories in those food. But after that timeframe, when I finally eat my regular food, I would gain the weight back. Therefore, I do not think of it as a "calories in vs calories out" rule simply because I would quickly regain the weight. What’s more important is the calories input within the timeframe afterwards that matters. If I were to fill up a bucket with water halfway today, and tomorrow I filled the rest with water, does it mean the bucket is still half full?
You calories input over an extended period is what matters, not the short run. Too many different factors come into play - genetics, body composition, energy use - when you just look at "calories in vs calories out." A healthy individual can get away with over eating in a day or two. However, if a healthy person ate donuts only for the next year, weight gain would be a huge possibility even though the calories input is not there. Again, it has more to do with diet over time, and not to do with diet on the short run. Eating one donut in the morning, while the rest of the day has “healthy” food isn't going to cause weight gain; your body burns the bad stuff in donuts, while the good stuff from the "healthy" food keeps your body in full function. But eating donuts all day, everyday, will increase the possibility of weight gain (depending on your body composition, genetics, age, etc) as well as the possibility of other health problems even though the calories is less - over time, you body thinks that food is the only available food so it begins to adjust and utilize the donuts and over time, your body is adjusted for donut usage and therefore, the system is now able to correctly break down and store material - ie. fat, muscle, etc - hence weight gain can be achieved.