I have previously asked about creating sub-dirs on under the Application directory and people have warned me that doing will can break things and it is not worth the effort.
The issue is that some updater programs are expecting to be able to update the program in its original install location.
This is actually regression in OS X. In classic Mac OS, you can move an application anywhere or even rename it and it will still work. Don't like the Application folder organization? Change it!
In OS X, you should be wary of moving any of Apple's applications, since Apple's Software Update seems to be the one that is most guilty of making assumptions. Lately I've been leaving programs dropped by installers in their initial location. But if the "install" is simply dragging an icon from a disk image, you are free to put it in any folder you want.
OS X will automatically find applications in the Applications folder and in any subfolder, and also it scans applications when you click on them. After that, it knows everything it needs to about that application's existence. Usually application paths are not important, so it is OK to move an application, aside from the updater issue.
Another way to create your own "Start Menu" type organization is to create aliases to applications and organize the aliases anyway you want.
The rationalization for why Macs don't have a Start Menu and Window does, is you'd never want users to have to wade through the Program Files folders, since they contains so much more visible files than just the ones you're supposed to run. The Mac has always tried to keep the applications self-contained, so the Applications folder only contains the icons that are of use to the user. If you present the Applications folder as a menu hierarchy it is what would be in the Start menu.