I think that part of the fun of cooking & baking is working with what you have, so my obvious answer is - of course!! But in order to substitute things without compromising flavour, you must understand the role of the ingredient in the recipe. For example, eggs hold things together. You can almost never substitute an egg. Salt brings out the flavour in each ingredient, so unless there are other salty ingredients (ie cheese), it should be included, especially in baking. Oil keeps the recipe moist - but thankfully, so does applesauce. It can be substituted easily.
To make things quite simple, I will put a giant NO SUBSTITUTIONS beside something if it absolutely cannot be substituted without wrecking the entire recipe.