For using as a raw topping, I slice onions in rings, thin enough so they will be partially cooked but still have a slight toothiness when done. If I'm caramelizing them, then I use thick rings so they don't cook down to mush.
I either cut bell pepper into long very thin strips or into slightly smaller than 1/4 inch square chunks, depending on what else I'm topping with. I like thin strips in a sparsely topped pizza, and chunks in a heartier pie.