How much "alternative" flour can I substitute for white wheat flour?
Mark Bittman actually includes a very handy quick-reference flour substitution table in How To Cook Everything (mine is the 10th anniversary edition, not sure if it's in previous editions). This assumes that the bread recipe calls for all-purpose flour and tells you how much you can substitute for the quantity the recipe calls for:


Whole wheat: use up to 50% in recipes
Rye:

light: up to 40%
medium: up to 30%
dark/pumpernickle: up to 20%

Cornmeal: up to 10%
Buckwheat: up to 20%
Rice: up to 25-30%
Nut: up to 25-30%
Soy: up to 25%
Spelt: up to 100%; then either decrease water by 25% or increase flour by 25%
Oat: up to 25-30%


The reason that different types of flours substitute at different ratios is primarily due to gluten content. Breads (both quick and yeast) made with alternative flours, especially non-wheat flours, will be heavier, denser, and less elastic; the substitution ratios above are meant to provide a nice balance between the nutritional and flavor advantages of the alternative flours with the texture qualities of all-purpose flour. For more information about the specific properties of each type of flour listed here, see the section called "The Basics of Flour" in How to Cook Everything (p. 835-838 in the 10th Anniversary ed.)

 Note: These substitutions are specifically for breads, where you want a sturdy, elastic structure. Low-protein or low-gluten flours may substitute at different ratios in other types of baked goods like desserts where you want a finer, more tender crumb. But I didn't get into that since the question was specifically about bread.