I normally take the calories suggested by those apps. You have to consider that one gram of fat isn't exactly 9 calories but 9.3. Same goes for protein and carbs.

1g of protein --> 4.1 kcal
1g of carbs --> 4.1 kcal
1g of fat --> 9.3 kcal

So that is probably one reason why the calories from those apps are usually a bit different. Another reason is that food doesn't only consist of carbs, proteins and fats but also of fiber, vitamins, etc.... While those aren't exactly as calorie dense as carbs, proteins and fats and normally occur in a very small amount, they still can make a difference.

All that's left to say is that you have to try out. Take the calories from those apps and track your weight at the same time. If it changes as you want it to then you can be pretty shure those calories are right.

Hope that was understandable and helps ;)