This is a very useful, unobtrusive, and beautiful app.
I use it primarily for organizing / arranging project-related files that are stored in various folders, so that I can see them all in one place easily. But basically you could use it for any kind of custom organization of your files and apps - arranging them independent of how they are arranged in your actual file system (i.e. what you navigate with the Finder).
For my purposes, it works much like "DragThing," but I found Berokyo to be easier to integrate into my workflow, more customizable and with superior aesthetics (i.e. it looks better). It also uses very little system resources.
Basically you can create one or many 3D "Cabinets" with "shelves." If you want, you can label / separate shelves according to categories, and each category can have subcategories. To put stuff on a shelf (anything with a selectable icon, like a file, app, etc.), you just drag-and-drop. It doesn't copy the file "into Berokyo," it just creates what functions like an alias/shortcut to it.
You can choose, on a cabinet-by-cabinet basis, to have a cabinet in "kiosk" mode or invisible when not in use. If the latter, you can choose to "dock it" on the top, bottom, left or right of the screen and made accessible by hovering your mouse at that location (or mouse+hotkey, your choice). In either case, you can also make your cabinet(s) appear with an assignable hotkey alone. The key for me was just reading the brief instructions (a very good "Getting Started" page is on their site and installs with the app) and learning the basic hotkeys to get going.
The one improvement I can think of is this: if you move the file that a Berokyo "shortcut" points to, it breaks the link. In that case you'd need to remove the shortcut and drag it again from its new location back into Berokyo. I'm not sure how all this works in the background, but I know other apps are able to "follow" a moved file to its new location.