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.}

With the no-knead, there is such good gluten formation that the texture will be quite similar even with half wholewheat. Past half, the liquid portion would need adjusting.

Buckwheat I find holds a lot of water but tends to dry out a loaf in texture: just wants to be crumbly and less 'juicy'. Start with 10% sub to be on the safe side. 20% will have a pronounced flavor like the pancakes (check out the proportion in Buckwheat pancake mix).

Flaxseed unground can be added liberally as the dough is coming together. It is really an addition not a sub for flour. Even 10% of the weight of the flour would be a very flecked dough. Most any bread recipe can handle that weight. Taste wise, a nice mix of seeds can go to 40% but requires a reliably strong well-developed dough to lift all that without becoming overly dense. Think sourdough.

Quinoa flour at 10% won't give you any trouble either. Fine cornmeal generally does make a loaf denser: holds water but doesn't hold the bubbles to allow as good a rise. Unless willing for big texture change, sub just a bit.

I've found in most bread recipes, you can replace up to 1/4 of the flour with another flour without problematic effects on the dough. Some recipes may allow a higher level of replacement, and of course it matters what you're replacing the white flour with. White whole wheat flour is very similar to white flour, but things like flaxseed flour are not, and the more similar, the more you can replace.

In some cases, such as replacing white flour with cornmeal, semolina, or rye flour, it will strongly affect the flavor of the finished loaf. But you should be able to follow the same instructions for kneading, rising times, shaping and baking as the original recipe. Some grains affect the amount of water required for the recipe, though (buckwheat and cornmeal are especially absorptive).

I've done this many times, with a variety of different recipes (batard, focaccia, sandwich bread, pizza dough, etc.).