Its one of those little things that can make the all the difference.
I manage a bunch of websites. By far the most confusing one is the one that has all the files stored in the root folder. Why is this so confusing? Because you cannot gain any understanding of the relationship between the files just by looking at the files and directory structure.
A properly structured directory structure can tell me so much about the files without reading them. I can guess what a file in "webroot/shopping-cart/google-checkout/callback" should do, even without opening the file. Finding and fixing bugs is so much easier in a properly structured directory.
As I began doing more and more of my new development in CFC's, this issue bothered me. I know how to instanciate an CFC in the root folder. Say you have a CFC "shoppingCart.cfc" in the root, you instanciate it like this: <cfset cart = CreateObject("component", "shoppingCart")>. But I didn't know how to instanciate a CFC in sub-folders.
As it turns out, its quite simple (that seems to be a ColdFusion mantra.) Say our shopping cart CFC is located in "webroot/siteComponents/cart/shoppingCart.cfc". To instanciate, you do this:
<cfset cart = CreateObject("component", "siteComponents.cart.shoppingCart")>
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