A calorie is a calorie is a calorie. To say they're different is like saying my kilometer is different to yours.
It's a unit of energy. You can measure it against a definition of it - e.g. a joule being related to increasing the temperature by 1 degree centigrade of 1 gram of water.
All calories are the same - but where you get them from can differ. They can be stored in different forms in the body.
Some obese people eat less than normal-weight people and yet still gain weight
because they use less calories than they take in... and you probably know people who eat a lot yet maintain their weight
because they have as many calories going out as calories taken in.
Healthier foods, giving a total of less calories in whilst having more calories out, gives a net negative balance, and so loss of weight.
Is there some actual data you can show, peer reviewed, accepted in the scientific community that's going to break thermodynamics as we know it? Because if it did, then we could use it to make a perpetual machine.
I think what muddies the waters, is that the body can have different rates of absorption of calories from food, can change it's metabolism. And that different foods can have different effects on the body.
Processed foods have been shown to cause changes to weight loss/gain on studies with mice for example - You are right in saying to stay away from alcohol (You can visualising this with the right equivalent- 1 shot of spirits is like taking a shot of cream calorie wise)
Other salt and sugar rich processed food can also affect the body negatively.
Eat the right foods. One isn't forced to choose healthier foods - you could do a guiness, bread and vitamin diet if you wanted to - but you're likely to look at veg and things more - as you can have bulk without the same number of calories, roughage etc to help feel full for example.
I recommend having a read of
http://en.wikipedia.org/wiki/The_Hacker's_Diet The Hacker's diet - free.
It shows why you need to look at a moving average to get rid of noise when looking at your weight on a day to day basis - and that tracking calories on a day to day basis is useful. Don't OCD, enjoy sporty things, and healthy food. Don't deny yourself completely either - are allowed a treat once in a while. If you'd rather go cold turkey - that's one way to do it. There are non-healthy foods, and thehre are non-healthy foods!
http://www.tgdaily.com/content/view/42366/181/