1. A single 0.6 oz Reese's peanut butter cup.
2. A large apple
By your logic, choosing the healthy apple will help you lose weight because it is not "crap", unlike the candy. However a large apple has 110 calories whereas a single Reese's peanut butter cup has only 88.
For the purposes of losing weight the Reese's peanut butter cup is the better choice. Arguably the apple has a better nutritional value, but that's not what we're talking about.
Also, I think it is important to not to focus on "losing weight", but living a healthier lifestyle.
Furthermore, telling people to count calories and not worry about the quality of what they eat is just opening the door for that same destructive human behavior of eating whatever crap they want, just in limited quantities. This is not the road to health. No amount of engineering mentality will get around the fuzziness of health or the stubbornness of human nature. Fortunately people are capable of being honest with themselves to varying degrees, and it is possible to improve one's health by a commitment to exercise and healthy eating.
The food you consume also interacts in complex ways that go beyond what has been formally quantified, but a casual observation of people who eat leaner foods and vegetables instead of processed sugars and dairy products is pretty good circumstantial evidence. There's a reason why dissociative diets can produce different effects on your body even though by the end of the week you may have eaten the same in terms of the amounts of calories and nutrients as other people.
I have two personal observations in favor of that: I have psoriasis, and the level and redness of the rashes is directly correlated to my daily intake of fruits and abstinence of coffee. I also know several people who are healthy vegetarians who have been keeping insanely good dieting regimes for several years, and it's remarkable how good their skin looks in comparison to other people of their own age, less wrinkled and more elastic (not being a scientific observation, my sample size is still large enough to be adequately convinced personally).
In fact, Apple(look at the nutritional values): http://en.wikipedia.org/wiki/Apple - Sugars 10.39 g - Fat 0.17 g
Peanut: http://en.wikipedia.org/wiki/Peanut - Sugars 0 g. - Fat Saturated 9 gr!! - Fat monounsaturated 24gr!! - Fat polyunsaturated 16gr!!
Maybe that doesn't tell you anything but 100 gr olive oil has more calories that 300gr of sugar.
Eating apples is natural for human beings,like many other fruits, eating peanut butter is not(apple has a lot of water with their sugar what makes it easy to process, and converting its sugars to fat would take energy).
They are other reasons for storing fat, e.g cold protection and cell and arteries protection from acids(produced by sugars burning).
The calories approach is an oversimplification.
With a small correction that eating apples that were not bred for sweetness and did not contain as much fructose as today's apples is natural. Therefore, there is such thing as too many apples (and fructose is probably not better than glucose or sucrose in any way).