Over the years I have developed a snobbery of eating that foods presented together should relate together in some way. While I wouldn't apply this to ordinary "family style" meals, for a special meal or at a restaurant, I think this is an important principle. It particularly bothers me when dishes are presented on top of each other in restaurants, such as a meat course on top of a vegetable course on top of a starch course. This has become very fashionable, but it is always a question of how one is meant to enjoy the presentation. Ultimately the best thing to do is deconstruct it, thus defeating the purpose of the presentation.
The main way I think courses should be related to each other is by having common ingredients. This can be as simple as including a squeeze of lemon in all the courses to be presented together, or using some other ingredient in common such as garlic or butter. It is more elegant when the courses are cooked in the same pan and pick up flavours from each other. Using vegetables to deglaze a pan that has cooked meat allows them to take on some of the savour and makes a better paired presentation. This is futher improved if a sauce is incorporated into both dishes.
Sauces are an important part of this principle. A lot of simple sauces and especially commercial sauces are prepared as separate components and only added to food at the very end or at serving time. There is no cohesion with the sauce in this presentation, and I can only presume its main function is to flavour an otherwise bland dish. The appropriate way to include a sauce is to incorporate it into the cooking of the dish. Pan sauces transfer the flavour left in the pan to the food it will be served with. Béchamel and similar sauces can be incorporated into the cooking process rather than simply poured over the top. Barbeque sauces should definitely be an integral part of the cooking, not simply slathered on at the end, when the lack of flavour transfer is particularly evident.
I even apply this principle to desserts like cakes and pies. Frostings should use an ingredient from the cake--not just the butter and sugar, but an intrinsic flavour such as vanilla extract or chocolate. Lemon Merinque Pie is a good example of a pie that shouldn't just have a meringue topping, but that topping should include the lemon used in the filling. The unification of flavours makes the dish much more stand-out than when the components are obviously separate.