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I'd actually recommend using a third of the flour as whole wheat flour instead of half like hektore recommended. He's right in that it will make things more dense and chewy, and not always in a way that has good results for a home baker's preference. Replacing only a third of the flour makes using whole wheat more workable in more recipes. You shouldn't use it anywhere where you would use pastry flour (low-gluten flour) but you can use it anywhere you'd use all-purpose, bread, or high-gluten flours.
In terms of baking bread, you will have to increase the amount of yeast used in the recipe slightly to compensate for the use of whole wheat flour if you do a 50/50 mix of white and whole wheat. When I bake our bread for the week here, I do a 50/50 mix but increase the yeast used from 2.25 teaspoons to 2.5 teaspoons (another reason to never buy yeast in packets). This is less of an issue with using whole wheat flour in pizza dough, as you're only doing one rise.
I'd say experiment with ratios. That is what led me to my 1/3 of the flour strategy--now I can sneak whole wheat into all sorts of things you'd never expect whole wheat in. And who knows--you might find, like I've found, that having all kinds of specialty flours on hand is not such a bad thing after all (at last count, I had six different different flours, and am adding a seventh to the collection [high-gluten for bagels] as soon as my kitchen is back together).
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If I am not better, at least I am different. --Jean-Jacques Rousseau
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