Keyboard buttons: Remember, you not only have the Programs, Quick Start, and desktop short cuts, but also keyboard button short cuts. More and more, keyboards come with buttons you can customize to access your frequent applications and folders. Anything with a keyboard shortcut should not appear in your Start, Quick Start or Desktop menus.
Start list: A few applications appear in the Start list (before selecting Programs). These usually contain the most recently accessed applications and a few others. This is a good spot for frequently used programs that don't have keyboard short cuts. Do you connect to your computer remotely? Then you might put some keyboard shortcuts into the Start menu since you can't access the keyboard itself through remote access.
Desktop shortcuts: This is the place to put less frequently accessed programs -- but not once every few months -- such as text editors, secondary browsers, business apps, and web-site related apps.
Program list: Put everything else in the Start > Programs list or remove it entirely. For example, you may have a "Coupon printer" application. You don't need that anywhere because it automatically comes up anytime you print a coupon using this application. It's unlikely you'll need to start the application yourself.