I'll keep adding to this list when I use ingredients that I think deserve a little more explanation than what I put in individual recipes
AP Flour (All Purpose Flour) - While I usually use bread flour in my breads, all purpose flour can be substituted in many recipes. AP has less gluten than bread flour. Gluten is the protein that forms the webby network that traps the gas bubbles that allow the bread to rise. AP flour might require a little more kneading before it's elastic enough. If you making a bread with a lot of other flours with little or no gluten, I recommend using bread flour or adding gluten to the recipe.
Bread Flour - A higher gluten flour. As far as brands, I use different ones, depending on availability and price.
Semolina - Often used in pastas, I like adding semolina to my white bread recipes. I like the depth of flavor it adds. You can find a coarser-ground flour and a finder-ground that's often labeled durham flour.
White whole wheat - a lighter colored wheat than standard red wheat, it gives baked goods a lighter color and a less bitter flavor than red wheat.
Protein Content in flour sold in the US varies by manufacturer, and sometimes by region. In general, cake flour has 6-8% protein; pastry flour has 8-10%; all purpose flour has 10-12%, bread flour has 12-14%, and first clear flour has about 15%.
I use kosher or sea salt for just about everything. Use whatever salt you prefer. I suggest that you don't eliminate the salt from the recipe. Saltless bread tastes dull and flat, but it also helps to regulate the yeast.
Sugars and Other Sweeteners
For most of the breads I bake, there's very little sugar, so you can generally substitute whatever you choose. Obviously, you'll get a little bit of flavor, and maybe some color, if you use anything other than white sugar. But unless there's a lot of the sweetener, it's not going to be a dealbreaker to use something other than what I ask for.
Honey - Honey is a great sweetener for bread, with one small warning. Honey has antisceptic properites, and some honeys can kill yeast. The first time you use a fresh jar of honey, make sure you test it with your yeast. If it proofs, then you shouldn't need to worry about the rest of the jar.
Honey Crystals - I found honey crystals at an Asian market. They're little round balls that taste like honey, but the ingredient list also lists cane sugar.
Honey Powder - Finer than the honey crystals, this is coarser than powdered sugar, but finer than granulated sugar, and tastes like honey. I found this at Savory Spice Shop, but it's probably available elsewhere.
Water and Other Liquids
Water - Unless your water tastes spectacularly bad or it's so highy clorinated that it might kill the yeast, plain old tap water should be fine.
Whey - in many of the recipes I make, I use whey. The reason I use it is because I have it and I don't want to waste it. The whey is left over from making Greek-style yogurt. Water is a fine substitute, unless you happen to have whey onhand.
Active Dry Yeast - One of the most common forms of yeast you'll find in stores. Active yeast need to be proofed before you use it.
Fresh Yeast - This is often hard to find, but if you happen to see it at a store, it's worth giving it a try. It has a short shelf life, so you should proof it before you use it. It's possible that they yeast you buy at a store is already dead. You can freeze fresh yeast if you buy it in bulk. After freezing, I'd suggest using more than you would have used fresh, since some of the yeast will inevitably die off during the freeze and thaw.
Instant Yeast - This yeast doesn't need to be proofed before adding it to your flour, but you can proof it if you want to. This is what I use most often. I buy yeast in bulk and this seems to be the most versatile.
Wild Yeast - This is the yeast you capture yourself (or you can buy strains of wild yeasts) for making sourdough breads.
Other specialty yeasts - There are some yeasts that are formulated to work better in sweet doughs. If you bake a lot of sweet doughs, it might be worth buying this. SAF Gold Yeast is one example.
For more in-depth information about yeast, see this post.
White bread and whole wheat are fine, but it's fun to play around with additions. I usually don't substite more than half of the white flour with the alternates, because I'm usually not fond of dense breads.
I'm always interested in using different grains in my breads. Besides hunting for optional grains at grocery stores, I always check ethnic stores to see if there's anything I haven't tried yet. Most recently I found some interesting malted barleys and other grains at a brewing store.
Mashed Potatoes (real or instant) - left over mashed potatoes or instant mashed potatoes are one of my secret ingredients in bread. They make the bread soft and fluffy, which is perfect for dinner rolls. I freeze 1/4 cup scoops of mashed potatoes on a baking sheet, and when they're frozen I put them in a zip-top bag and keep them in the freezer until I need them. The instant mashed potatoes are great to have onhand when I don't have leftovers. I look for a brand that has the fewest ingredients, and I've been lucky enough to find some that are nothing more than dried potatoes.
But how do all these ingredients affect the dough?
I've compiled this list from a variety of sources in books and online.
Ash content (minerals in the flour) - The percentage of minerals in flour changes the way the dough reacts. European flours are labeled by ash content, while American flours are labeled by the amount of gluten. Higher ash means stronger dough and more food for the yeast.
Ascorbic acid (vitamin c) – Strengthens the gluten. Dough can be baked at a higher proof level.
Baking powder - Some breads include this as a secondary leavening agent.
Beer - Creates a supple dough.
Beet water - Colors the dough; bread will be a rosy color.
Butter, oil – Lubricates the gluten and increases loaf volume. Bread will have a softer crumb and crust, and a longer shelf life.
You get a better gluten development if the fat is added after the dough has been kneaded. If fat (particularly solid fat) is added to the dough too early, it can coat the flour and keep the gluten from forming.
Too much fat will result in a compact loaf because the fat over-tenderizes the dough and retards yeast.
Buttermilk - The acidity strengthens the dough.
Cinnamon - Increases yeast activity in small amounts; retards yeast in larger amounts.
Cardamom - Increases yeast activity.
Diastatic malt (malted barley flour) - Converts starch to sugar; helps feed yeast. Too much will result in sticky gummy bread, and an overbrowned crust.
Dry mustard - Inhibits yeast activity.
Eggs, whites only - Lighter texture.
Eggs, whole - Enriches dough. Also, dries dough out; egg-rich doughs usually have a lot of sugar, which retains water to counteract the drying effect.
Ginger - Boosts yeast, keeps bread fresher longer, deters mold and bacteria. Just 1/4 teaspoon per loaf is enough to affect the dough without a noticeable flavor.
Gluten - Can be added to non-wheat flours. 1 tablespoon per cup of flour is enough. You don’t want to add too much gluten; it’s not needed in breads that are made primarily of wheat flours.
Gelatin - Helps texture and moisture. 1 teaspoon per loaf is enough.
Garlic - in small amounts, helps the yeast, make dough easier to roll. Acts as a preservative, and deters mold and bacteria.
Honey - More golden crust than sugar, keeps bread moist. Honey has antibacterial properties and retards mold. Some honeys can kill yeast, so it’s wise to proof the yeast with any new jars of honey.
Lecithin - Extends shelf life, preserves flavor. More lecithin softens the crumb; and produces a finer texture and more tender crust. Lecithin is in egg yolks and can be purchased as a powder or granules.
Milk - Strengthens gluten, helps crust brown, softens the crumb. An enzyme in milk slows the growth of the yeast and it can break down the protein in the flour and weaken the dough. Scalding the milk destroys this enzyme.
Milk, dry or powdered - Improves crust browning, adds moisture. Helps the dough to relax.
Non-diastatic malt (barley malt syrup) - Flavor and sweetness only. Does not affect the yeast.
Nutmeg - Increases yeast activity.
Pectin - Adds moistness and can replace fat in bread. 1 teaspoon per loaf is enough.
Potato water - Keeps bread moist.
Salt - Regulates yeast, strengthens and tightens gluten. Too much kills yeast; tight gluten can make dough harder to knead, so some people add the salt after the dough has been kneaded for a while; others think that it’s too hard to distribute the salt if it is added too late.
Sour cream - Acid strengthens dough; fat tenderizes the dough.
Soft cheeses - Adds moisture and flavor.
Sugar - Feeds yeast, holds in moisture, keeps crumb softer, keeps bread fresher. Too much can retard the yeast.
Thyme - Increases yeast activity.
Vinegar - Yeast enhancer in small amount. Retards yeast in large quantities.
What you put on top of the loaf makes a difference.
Butter - Soft velvety crust
Cornstarch and water, cooked - Very shiny hard crust.
Dry oven, no water on crust - Soft crust.
Dusted flour - Powdery rustic chewy crust.
Egg and heavy cream - Shiny deep brown crust.
Egg and milk - Shiny medium brown.
Egg white and water - Crisp light brown crust. Good for sticking toppings onto the bread.
Milk and sugar - Soft sweet crust.
Water (sprayed or brushed on the bread, or as steam in the oven) - Crisp crust.
Whole egg and water - Medium-shiny golden crust.
Depending on how you measure all purpose or bread flour, it can weigh anywhere from 4 to 5 ounces per cup. For my recipes, I've decided that a cup of all purpose or bread flour weighs 4 1/2 ounces per cup. However, if it is sifted before measuring, it weighs 4 ounces per cup.
White whole wheat flour, depending on brand, also weighs about 4 1/2 ounces per cup, and I've decided to use that as my standard.
Semolina flour is heavier. I originally used 5 ounces per cup, but after testing several different brands, I've settled on a standard of 5 1/2 ounces per cup.
Rye, whole wheat, and specialty flours vary in texture depending on how coarsely they're ground, which affects the weight. I always weigh and measure them when I'm writing a recipe.