My favorite pizza is napolitano con cipolle - naples pizza (tomato, mozzarella and anchovies) with onion - here it's always made (any time i've had it) with raw thinly sliced onion strewn on top of all the rest, and the heat of the oven (which has to be very high) cooks the onion, getting the edges slightly burnt, only slightly. very tasty.
However, pissaladiere (or pissaladina) - the provencal pizza - is wonderful too, and there you sautee the onions in olive oil slowly till they're soft, then put tehm on the white pizza dough (no tomato) with anchovies (preferably the ones packed in salt, not oil) soaked and washed of all the salt, and black (not canned!) olives. very tasty. I never saw an italian pizza with cooked onions, however.