I am obsessed with sorting my apps into folders; if I didn't, it would probably take an hour to display the contents of my Applications folder. Unfortunately, Apple's built-in updates, as well as those of some other developers, can only take place if the application file is directly in the Applications folder. To get around this I have been using aliases and hiding the originals using JuhOS X, a visibility toggling application that requires navigating through a folder hierarchy each time I'd like to use it.
GoodbyeHello makes visibility toggling for specific directories much more efficient. All that's needed is a drag-and-drop onto the application's icon, and – assuming I have the necessary permissions – the file has vanished from view. GH also provides the option, in its File menu, to navigate to the desired visible or invisible file, folder, or path, and toggle its visibility that way. (Invisible items are visible in the navigation window when visibility is being turned back on. As you would hope them to be!)
Sam's Protip: Place GoodbyeHello in the Finder toolbar – as I have done in my screenshots – or in the Dock for optimal accessibility.