Take some real world examples:
I want to examine the services running on my Windows XP machine. I can never remember if I use:
Start -> Programs -> Accessories -> System Tools
Start -> Programs -> Adminstrative Tools
is it on the Control Panel?
You get my point. There's no logical way for me as a user to understand the Taxonomy that resulted in Microsoft putting the Services in Administrative Tools.
Windows 7 and Apple now have very good search mechanisms on the Desktop. Spotlight on the Mac is my primary navigation mechanism. I never try to find a file or a program by navigating through a hierarchy. You can generally always find it by typing in a few characters, and letting search do the rest.