I think the question doesn't need more explanation, just if you have to add any seasoning, from pepper to any other kind, specially if you have a variety of them, do you decide an order for them?
Yes it does make a difference when you add the seasoning. The taste varies depending on when the seasoning ingredients are added. As for as stir fries or any dry fries are concerned, it doesn't make much difference. But in water based dishes like sauces, curries, gravies, and soups it could impact a great deal. The water absorbs the spices added , making its flavor incorporate completely. Also the raw smell of the spices vanish to a great extent if they are added at the beginning. Also in case of pepper in gravies and other dishes, the sooner it is added, the hotter the dish becomes after a considerable amount of time. It is due to the time taken for the spice to infuse the flavor/taste completely through the dish. Dishes based with vegetables, the sooner you add salt, better the vegetables absorb . They could be bland if salt and spices are added last. In India, in most of the curries masala (ground mix of spices, like cloves, cardamom, cinnamon, fennel ) is sprinkled at last to give the dish an extra flavor, though it is also added in the beginning during preparation.
Hence taste could vary depending upon the time you season the dish. There may be exceptions. But that is the general theory for most of the dishes.
Some herbs lose a lot of taste when added too soon, other spices need time and heat to give off their full power.
For example when cooking a curry I always add the spices first into the heating pan, then add onions, ginger, garlic and then oil and let it all fry a little. Only then do I add moist ingredients because those flavours would never develop when just adding the same spices to water or tomato sauce. If I later feel I have too few spices I sometimes even take a new pan, make a fresh mixture and add it to the first instead of just adding more spices.
But if you make tomato sauce for pasta and you add your basil too soon all it does is add little green bits, because the flavour doesn't stand too much cooking.
A little bit over-simplified:
- Fresh herbs later (some as late as on the plate)
- spices or died herbs earlier (for water based dishes maybe before adding the water)
But I feel that adding a list with all spices with a time to add would be too much for this site and rather fill a book.
Apart from herbs and spices (covered in other answers already), the timing of when you add:
sugar (which can caramelize or mess with osmosis if added early, stay gritty if added too late),
salt (osmosis again, grittyness again),
acids and bases (citrus, vinegar, baking soda... influence how some ingredients will cook. Also, citrus juices will change flavor when cooked),
alcohols (flavor extraction, evaporation),
watery extracts (eg soy sauce, broth - they can reduce and even caramelize/burn, or dilute the cooking liquid, or get infused deeper into ingredients)
matters. These are all part of seasoning too if used.