I use Cronometer (www.cronometer.com) and a scale. It lets you create recipes with the weight of each item and the weight of the final result. I then weigh the portion I have with a meal. Why do I do this in the first place? I'm one of those people that eats too little vs too much, especially in the summers when I'm outside all day burning tons of energy: tracking calories helps me keep weight on. I have to eat so much food to maintain my target weight that it gets pretty uncomfortable some days. Yay for muffins and cookies.

Don't worry about how leftover nutrients decrease over time: you'll get enough nutrients in a well balanced diet without having to worry about the minutia. If you're really worried about it, pop a multivitamin for cheap insurance.

Also don't worry about the variation in calories between one type of cucumber / apple / whatever vs. another. Those variations aren't significant and they probably average out anyway. Realize too that the sources aren't exact in the first place: once source is likely to give a different caloric value for something like dried beans vs another.

If you're going to track, don't get too caught up worrying about if the absolute value of the calories you're recording is 100% accurate because even if they were, you can't track your energy expenditure 100% accurately. If the bathroom scale goes in the wrong direction for you, adjust your caloric intake to compensate. Look at trends over the week and over the month vs day to day variations and it won't take long to zero in on the right number for you.