There is no chemical difference between adding salt early or late in the cooking process. However, if you salt just before eating, you can take advantage of textural differences between different types of salt. (Kosher salt is flakier and so gives a burst of saltiness that is quite pleasant.) (Some people will say that you should salt earlier to bring out flavors more, but once the salt is dissolved in solution, the chemical effect is the same.)
In general, fresh herbs tend to be added later in the preparation -- with the exception of parsley or dill added to soup early on to flavor the broth. However, if the herbs are added early, they must be removed, since they will lose all their flavor. (The broth will gain flavor, but the herbs will be exhausted.) You'll maintain the bright flavor if you add them late.
Dried herbs tend to react better to longer cooking, with bay leaves in particular requiring lots of time to render out their flavor.
As far as pepper goes, there's a fantastic answer to this question that goes into the chemistry of the volatile compounds in the spice. In general, I find that I prefer adding pepper later in the cooking process.
Garlic, ginger, onions, and other aromatics can be cooked a long time, although the flavor of alliums will change enormously as you cook them. (Garlic, in particular, will change enormously from a sharp flavor when raw or quickly cooked to a rich sweetness when cooked a long time.)
Stewing or braising is essentially what slow cookers do, so there is not a huge difference in converting a stew recipe.
There are two main issues to consider:
Flavor development. You may choose to sear or brown your ingredients separately, and then deglaze for your base sauce. Most slow cookers cannot create the browning, so it would need to be done separately.
Liquid level. If your original recipe stews with an open lid, you will get less evaporation in the slow cooker, so may want to reduce the liquid slightly to compensate.
Best Answer
As a general rule they should go in early for a couple of reasons:
Flavours don't really cook out, they get distributed within the dish. So adding spices etc. early allows the flavours to combine. If they did cook out you could just add a touch more.
Opening a slow cooker during the cooking time lets write a lot of heat out, at best extending the cooking time. Repeatedly opening it from early in the cook (worst case) would bring the temperature down too far. So you either add things at the beginning or at the end (when the food is already cooked and hot enough all the way through that it will stay at a sensible temperature). This allows final fine adjustment at the end, but you may need to be choosy about the form in which you add the heat - some things could be hard or gritty if they haven't cooked. Fresh herbs can be added just before serving as they don't need to cook and may lose some of the fresh components of their flavour.