There are all kinds of possibilities for replacing wheat flour in baking. There are several types of nutritious grains, seed flours, flour made of coconut, sweet potato, even grapes...endless options that are healthy!
If you are starting out learning how to replace wheat flour, here is what I recommend:
As a rule of thumb, no single flour will adequately replace wheat flour. Combinations of flours work well together.
If you can have oats, use them! Regular or quick oats can easily be ground into flour in your blender. This flour is economical, very nutritious, and has a mildly sweet flavor and gummy texture that complements rice flour very well. Rice flour by itself is grainy and bland, and also dry. Oat flour by itself produces heavy, dense, and gummy products, in general. Together, these flours have traits that work together very well.
When I adapt a recipe using wheat flour, I almost always bake with either a nearly half and half ratio of brown rice flour and oat flour, or a combination of brown rice flour, oat flour, and bean flour(usually lentils ground in my blender). With these flours, I do add tapioca starch and xanthan gum as part of the measured amount of flour. Since tapioca starch and xanthan gum have sticky properties, and oats have gummy properties, I include the measure of tapioca starch and xanthan gum in my measure of oat flour, so that the full cup of rice flour can offset with its grainy properties. 1 Tablespoon tapioca starch/flour per cup of gluten-free flour is a widely used rule of thumb. A common rule of thumb for xanthan gum is 1/2 tsp per cup of gluten-free flour for cakes, cookies, and muffins, and quick breads, and 1 tsp per cup flour for yeast breads. In general, then, if a recipe calls for 2 cups wheat flour, I measure 1 cup of brown rice flour, and then measure 2 T. tapioca starch and 1 tsp. xanthan gum in a 1 cup measure, then fill the rest the way with oat flour. Actually, since oats do have some gluten and they do have properties more similar to wheat than non-gluten flours, I do sometimes add just 1 T. tapioca starch and 1/2 tsp xanthan gum to a recipe with 2 cups flour. I'm experimenting with this. UPDATE from Nov 2010: check out my homemade baking mixes post- this simplifies things!
Xanthan gum helps the product to be much less crumbly, have an overall better texture, and have longer shelf/freezer life. Tapioca also improves texture, helps lighten the product, and makes a nice springy crust.
When using bean flour in a recipe, I don't quite use the 1/3 ratio. What I do is add cornstarch, potato starch, or tapioca to the measure of bean flour that I use. So, in a recipe calling for 3 cups wheat flour, I would add 1 cup brown rice flour, 1 cup oat flour, and then fill up a 1 cup measure with first tapioca starch(maybe 2 T.), then some potato starch or cornstarch(maybe 2 T.), then 1 tsp. xanthan gum, then the rest the way with bean flour. Or, I may use 1 1/2 cup. brown rice flour, 1 cup oat flour with the tapioca/xanthan gum rule of thumbs included in the measure, and then 1/2 cup bean flour.
I find that when I experiment with different ratios of flour in muffins or fruit/vegetable puree cookies(banana, pumpkin, etc), these products are pretty flexible. I end up with different results, but most my experiments are satisfying. I don't mind ending up with a muffin a bit on the dense side, as long as it has a good flavor, texture, and tastes wholesome! When I adapt a recipe, I record the changes I make, make note that I'd like it to be less dense next time, and decide what to tweak in the recipe to try to achieve an even better product. I have a notebook dedicated to recording my adaptations and results. I'm much more laid back about experimenting with food than I used to be, since I've discovered that most any "flop" you may have can be converted into something good. And I'm learning which types of products have more experimenting leeway(like muffins), and which products have less leeway(like yeast bread).
Because I use whole-grain oat flour, brown rice flour, often bean flour, and then just a little bit of starch when I bake wheat-free, the baked products that result are very wholesome and satisfying. These combinations of flour work very well for muffins, waffles, fruit cookies(banana, pumpkin, zucchini, etc), and quick breads(banana, zucchini, etc). Fruit crisp, oatmeal cookies, and oat pie crust work well with oat flour replacing all of the wheat flour in the recipe.
Oat flour, brown or white rice flour, and many assortments of bean flour are available at many stores. If the grocery stores you shop at don't have them, Whole Foods Market carries them. These can all be produced at home, however, at a much better price! Oat flour is easily made from grinding rolled oats(quick or regular) in a blender. Lentils also grind in a blender. Depending on how good your blender is, lentil flour may be a little course in texture, but still okay. A VitaMix machine works great! If you're serious about wholesome nutrition, a VitaMix machine really can pay off in initial cost. Especially for a family with allergies or food sensitivities. I use mine for grinding batches of flax seed(egg substitution), prunes or other fruit/vegetable purees(egg or dairy substitution or use in cooking), sunflower seed butter, lentils, hummus, countless whole fruit smoothies and whole fruit/vegetable juice, etc... I use my VitaMix nearly every day, and often a couple times in a day!
If you get a special container designed for grinding, you can use a VitaMix to grind rice and other grains into flour. You may want to look into buying a grain mill if you don't own one. Initial cost is high, but it could really pay off in nutrition and overall savings. Price ranges are broad, mine was $150, as it was used, but has worked great. I grind large batches of brown rice and oat groats into flour, and then store the flour in gallon-size freezer bags or in various containers in the freezer. Last year I used 50 lb brown rice, between baking and serving cooked, which I believe I paid about . 50/lb for. One year's worth of rice flour, then was only about $25! Brown rice has gone up in price, but still can be a lot cheaper to buy than to purchase already made brown rice flour. Oats are very economical. I can get a 25 lb bag regularly for .39/lb. Even if you find a sale on a 42 oz. container at $2.00(last year they went on sale for $1.00 at Smith's, but that was last year), that is still only about .75/lb.
I have tried a few different gluten-free flour combinations, and also a couple purchased gluten-free flour mixes. The most basic combinations tend to be rice flour and starch such as tapioca and potato starch. By itself, this combination of flour is bland. Also, tapioca and potato starch have 0 grams protein, no fiber, and a lot of carbohydrates. With these mixes, other ingredients in the recipe are important for flavor and nutrition. I have made a yummy chocolate cake from a gluten-free mix, using yogurt instead of milk and flaxseed instead of egg.
There are several things you can do to boost the nutrition value of a gluten-free product, including adding flaxseed meal or baking with fruit or vegetable purees. Most notably, Carol Fenster and Bette Hagman, among other gluten-free experts, have found that bean flour such as garbanzo bean flour, or garfava bean flour or sorghum, really can improve the basic gluten-free mix of rice and starches. These bean flours add a mild flavor, improve texture, and definitely boost nutrition of the flour mix. I am pretty satisfied with a yeast bread recipe that calls for a few kinds of bean flour. It's actually my favorite yeast gluten-free bread that I've baked. It's called Flax Seed Four-Flour Bean Bread, by Bette Hagman. It uses a mix you can make at home: 3 cups Garfava Bean Flour, 1 cup Sorghum Flour, 4 cups Tapioca Flour, 4 cups Cornstarch. I'll post the recipe. UPDATE from Nov 2010: I have a new favorite bread recipe, see my post "Really Good Yeast Bread!"
If you cannot have oats, I recommend looking for flour mix recipes or products that have bean flour in them. Carol Fenster and Bette Hagman have recipe books that you could check out at your local library. They have several basic flour mixes that you can make at home and store in bags, for easy use in recipes. Several gluten-free bloggers post these flour mix recipes as well. In my post, "Flours to replace wheat," I have posted a garbanzo-bean flour mix that I have liked.
I often bake with lentil flour. Actually, I rarely bake with any other kind of bean. This is because I can make my own lentil flour at home in my VitaMix(or blender), for a much better price than purchased bean flours. I hesitate to make bean flour at home other than lentil or split-pea, because other beans are supposed to be soaked before cooking. I hear you can bake with home-ground beans such as pinto, etc., but the flavor is stronger, can be bitter, when compared to purchased bean flours that have been processed. Molasses can help, I hear, if you make and use your own bean flour. I just go with home-ground lentils. They're really nutritious, too!
UPDATE from Nov 2010: I like to bake with white bean flour as well as lentils. I've seen several places where people bake with bean flour other than lentils. The white beans I grind in my grain mill. They can be ground in the VitaMix as well, or even in a cereal grinder that I tried at my Mom's. The white beans haven't been too strong in flavor. I do add a little molasses when I bake with white beans(@1/2 tsp. blackstrap for most baked goods), but if you don't have any, I would try without.
The Living Without magazine has a page called Living Without Pantry Substitution Solutions. It is available online at livingwithout.com, and has four different gluten-free flour mixes. It adds direction as to which type to use for which purpose. It has a basic mix, a high-protein mix, high-fiber blend, and a self-rising flour mix.
For exploring baking with alternative flours not mentioned on this post(amaranth, teff, coconut, cabernet, etc), see my post "Flours to Replace Wheat." There are a couple of books I recommend that give the properties and best uses of several different flours, as well as ratio amounts of how much of a particular flour to use in a recipe. Livingwithout.com has a few different articles that help one to be familiar with a wide array of flours available to replace wheat. Search under "past articles."
If you are not used to whole-grain products but you want the nutrition benefits of them, try baking with a combination of white rice flour and oats to begin with(together with any tapioca/cornstarch you might include). Then, replace half of the white rice flour with brown rice flour. Bake this way for a while. Finally, replace all of the white rice flour with brown rice flour. The brown rice flour is so much more nutritious, and has a nicer, nutty flavor. The only time I would use white rice flour, now, is for delicate, fluffier items such as a white cake. In yeast bread I might use part white rice and part brown rice flour.
In cooking rice for serving at a meal, your family can get used to brown rice. I used to only cook white rice for my family. We enjoyed it. I started cooking half brown and half white together, and we got used to that. Then we only had brown rice, and we got used to that. I ran out recently, and have gone back to cooking white rice, until I buy more brown(I'm searching for the best price out there on a large amount). I do not enjoy white rice anymore! My husband says he wants the brown back, he likes the brown as much as the white now, and he likes the nutrition benefits of the brown so much more. If you do not like brown rice right now, you can definitely gradually get used to it. You may find that you prefer it over the white rice! note- my kids still do seem to prefer white rice : ) but they eat the brown as I serve it : )