It depends on what you want for flavor and what you are putting them with.
A raw onion cooked on the pizza can give you a sharp, fresh spicyness to contrast other flavors, not to mention texture.
An onion changes character when sauted. The texture changes and they can beconme sweet. This is great if it fits whith what you want.
Carmelized onion with roquefort and pears. You get the tooth from the pear, the sharpness from the cheese, and the onion is a nice background texturaly and flavor wise.
Pizza with wild mushrooms, fontina and onions. This might be nice with very thin raw onions cooked with the pizza. They would give a nice texture contrast and a sharpness of flavor.