Windows only: Desktop icon organizer Fences arranges your cluttered desktop icons into containers so you can clean up the mess into useful groups of shortcuts—or optionally hides them altogether. Once installed, Fences will run through a couple of first-time beginner screens asking if you'd like to use one of the built-in layouts, and will attempt to auto-detect which icons should be placed inside each fence.
Windows: From the creators of Fences comes Bins, which is basically the Windows 7 equivalent of the "Stacks" feature in Mac OS X. If you want to organize your taskbar's program icons into little convenient bins, this download is for you.
Windows only: Customize or clean out your cluttered right-click shell menu with freeware application ShellExView.
Windows only: Free file-copying utility TeraCopy speeds up file transfers and can pause, resume and test file copy operations.
Windows has a ton of great utilities, and while we can't live without some of them, there's a special place in our heart for programs that merely improve Windows, rather than adding new software.