What are the most effective wheat flour substitutes?
Wheat Flours at Cook's Thesaurus discusses varieties of wheat flours and their substitutions in general baking, yeast breads, and as breading agents.

And here's a reference discussing "the carbohydrate-content, dietary fiber content and 'net carbs' in all types of flour": Carbohydrates in Flour and Baking Foods.

I consult these pages as jumping off points when I'm altering my baking recipes. I'm a big fan of mixing flours to come up with lower-carbohydrate and more nutritionally sound baked goods (white flour isn't the most nutritional option out there, no matter that it's one of the most common options in baking). Oat, spelt, and soy flours figure in a lot of my recipes (note that using soy flour calls reducing the baking temperature called for in a recipe by 25&deg;F, and that soy has a very pronounced flavor that not everyone likes).

The more you learn about the various flour options, the easier it is to make substitutions with confidence, so I encourage you to do a bit of reading. Of course, if you're rushed, baking sites (ones that sell high-quality flour, such as Bob's Red Mill) tend to tell you right on the page how much of their flour to substitute for wheat flour.

As a general rule, the more whole grain flours you use the better because of their higher fiber contents. If you subtract the fiber from the carbohydrate count, you find the net carbohydrate of the flour in question, and it's the net carbohydrate that tells you how your sugar levels will be affected. One carbohydrate serving is 15 grams of carbohydrate total. 

One cup of all-purpose flour has 95 grams of carbohydrate and 3 grams of dietary fiber, which gives each cup a net carbohydrate amount of 92 grams (which is 6.13 carb. servings). One cup of whole wheat flour, on the other hand, has 87 grams of carbohydrate and 15 grams of dietary fiber, which gives each cup a net carbohydrate amount of 72 grams (which is 4.8 carb. servings). Even if you're baking a bread that isn't particularly low in carbohydrate, getting the benefit of the increased nutrition and fiber from a whole grain flour will benefit you.