Butter
To be fair, this section ought to be titled "shortening." After all, butter is not the be-all and end-all. Vegetable shortening, margarine and, in rare cases, oils have their place in the cookie world. Ask most experienced bakers, though, and they will tell you that one of their secret weapons is plain, pure butter. Inexperienced cooks are sometimes confused because many cookie recipes call for unsalted butter and salt -- heck, why not just kill two birds with one stone and buy regular salted butter?
Butter -- or other shortening -- serves several purposes in a cookie. It tenderizes, giving most cookies that wonderfully rich, melting quality -- you'll find that hard, crispy cookies such as biscotti have a lower butter content than other types. Most important, as any food chemist will tell you, fat is the single best conveyor of flavor -- better than sugar, better than flour, better than anything, hands down.
When you put something in your mouth that has a fairly high proportion of butter, the butter coats your taste buds with every flavor present in the cookie. It's a rich, divine experience, and it helps explain why people love cookies so much.
And, as baking purists will tell you, unsalted butter tastes fresher because, well, it probably is fresher. Salt is a preservative and was originally added to butter in the days before refrigeration was widely available. Salted butter keeps longer and has a wider "sell by" or "use by" range, so it doesn't necessarily get sold or used as quickly as the unsalted version.
In its lifetime, salted butter may develop an "off" flavor as it absorbs the smells of everything, from the factory in which it was produced to the packaging in which it was shipped to the foods inhabiting your fridge.
Long story short: It's really best to stick with unsalted butter. And do not under any circumstances try the reduced-fat "spreads," which can contain as much as 58 percent water and are totally unsuitable for baking.
Sugar
The use of sugar in a cookie is obvious -- cookies need sugar to taste sweet, whether cloying or subtle.
The other purposes of sugar are less apparent, but equally important. Sugar is hygroscopic, which means it draws moisture or water to itself. In addition to its sweetening properties, then, sugar helps make cookies tender and soft.
Beyond this, sugar absorbs heat, which helps cookies to brown.
The two most common types of sugar used in cookie baking are regular granulated white sugar and brown sugar, be it light or dark. Their sweetening properties are roughly the same.
It used to be that white sugar had gone through a more thorough refining process than brown, so that brown sugar had an earthiness and a depth of flavor lacking in white sugar.
These days, however, brown sugar itself is fairly refined and may get its color from molasses being added to it after processing. The molasses, because of its high water content, helps brown sugar have stronger hygroscopic properties than white sugar. This is why, in addition to some flavor benefits, brown sugar and white sugar are often used in tandem in cookie recipes -- they both help to sweeten, and the brown sugar boosts the moisture-holding properties of the white sugar.
FlourFor cookie baking, most folks stick to wheat flour. The amazing variety of other flours out there -- from potato flour to nut flours to corn flour and beyond -- are generally unsuitable for use in cookies.
Wheat flour, however, has its own subcategories. Virtually all cookie recipes call for all-purpose flour. The addition or substitution of other flours, such as cake flour, bread flour, self-rising flour or whole wheat flour, is generally not recommended -- at least, not until you peruse the guidelines that accompany this article. That's because each type of flour has an individual protein profile suitable almost exclusively for specific uses.
Bread flour, for instance, has a higher protein content than all-purpose -- all the better to develop the strands of gluten which give bread its characteristic chewiness. Self-rising flour, on the other hand, while popular in regional pockets of the United States -- especially in the South -- is not generally recommended for use in cookies because people often forget that it already contains leavening agents, accidentally add them, and then wonder why their cookies came out funny.
Generally speaking, unless a recipe indicates otherwise, you will do best to stick to the straight and narrow all-purpose flour road.
Other ingredientsLeavening agents are an important part of most cookie recipes. The most commonly used leaveners for cookies are baking powder and baking soda.
Possibly the single biggest culprit in cookie failure is the tendency of the cook to misread which one is called for -- and add the wrong one.
The big difference between baking soda and baking powder is that baking soda requires the cookie dough to have at least one acidic ingredient, while baking powder has its own acid built in as acid salts -- cream of tartar, usually.
You'll find that baking soda tends to come to the fore in recipes that use sour cream, lemon juice, yogurt or buttermilk. Baking powder tends to be used in recipes that have no acidic ingredients, or call for chocolate or cocoa.
A good rule of thumb to remember: 1/2 to 1 teaspoon of baking soda for each cup of liquid and 1/2 to 1 teaspoon of baking powder for each cup of flour.
An easy memory device is that SODA goes with liquid and POWDER goes with flour.
Eggs are another common cookie leavener, but their main job is to serve, frequently, as the only liquid in the ingredient list. Egg whites tend to dry out cookies, while egg yolks enrich and soften the dough.
TinkeringHere's one way understanding cookie chemistry comes in handy -- you can tinker and fool around to your heart's content to get the cookie exactly the way you want it.
Warning: We don't recommend that you try this with a new, untested recipe -- use this guide to help you adjust a recipe you've already made so you know what the original was like and what you'd like to change.
And be sure to adjust ingredients, baking times and other elements gradually, preferably one or two at a time. You'll find that sometimes simply tweaking something by a tablespoon can make an enormous difference. These tips are gleaned from Shirley Corriher's 1997 "Cookwise" (William Morrow, 1997).
High-protein flour: Makes cookies darker in color and flatter.
Low-protein flour: Making cookies pale, soft and puffy.
Fat with sharp melting point, like butter: Makes cookies spread.
Fat that maintains same consistency over a wide temperature range, such as solid vegetable shortening: Makes cookies that do not spread as much.
Corn syrup (or molasses): Makes cookies browner.
Brown sugar and honey: Makes cookies that soften the longer you keep them.
What to do if ...
You want the cookies to spread more: Use all butter OR add 1 to 2 tablespoons liquid (water, milk or cream -- not egg) OR use a low-protein flour such as bleached all-purpose (but not one that is chlorinated) OR add 1 to 2 tablespoons sugar.
You want the cookies to spread less: Use solid vegetable shortening or substitute some solid vegetable shortening for some of the butter OR use an egg for liquid OR use cake flour OR cut the sugar by a few tablespoons OR switch from baking soda to baking powder OR chill the dough before baking it.
You want the cookies to have a chewy quality: Melt the butter instead of simply using it at room temperature.
You want the cookies to have a cakey quality: Use the butter at room temperature or use equal parts butter and solid vegetable shortening.
You want the cookies to be more tender: Use cake flour OR add a few tablespoons of sugar OR add a few tablespoons of fat.
The cookies are too tender and you want them to be more substantial: Substitute a few tablespoons of unbleached or bread flour for the all-purpose flour OR cut the sugar by a few tablespoons OR cut the fat by a few tablespoons OR add a tablespoon or more of water to the flour before combining it with the other ingredients.
You want the cookies to brown better: Substitute 1 to 2 tablespoons of light corn syrup for the sugar OR use an egg for liquid OR substitute a few tablespoons of unbleached or bread flour for the all-purpose flour.
The cookies are browning too much, despite the correct oven temperature: Substitute water for all or some of the liquid ingredients OR use cake flour or bleached all-purpose flour
While your dough is chilling in the fridge, start to assemble the ingredients for the next step. You'll need: 
