I know this is an old post but I will reply anyways. My rule of thumb has always been what ever topping needs the most cooking should always go more towards the top. For example Pep needs almost no cooking so it always first on, cooked bacon or ham may be next and so on. Veggies are the same way, olives, pickled peppers and things like that first and raw veggies in order of cooking time. Mushrooms cook quicker then onions and raw peppers normally take the longest. Any raw meat should always be on the top if you dare to use such a thing (raw sausage cooked on a pizza is wonderful as long as it cooks all the way).
This is sort of a personal topic but this is how I always work it, of course as Bob says if you want something extra crispy you should put it on top. I know I do a hot dog pizza for the kids when I am having a party. It is pretty much dough topped with a mixture of 5 parts ketchup to one part mustard as the sauce. A cheese blend that must include cheddar, and then Hot dog, followed by what ever vegetable(s) I can get the kids to agree on and then topped with diced left over bakes potato. The Potato is always on top not because it needs to cook longer but because I want it to be more crispy and brown like french fries might be. The kids always like it and then I can go back too making more fun adult pizzas with things like capers and goat cheese on them.
