While I now try to keep most of my written personal information in a single text file, I have a lot of external reference material (e-books, articles etc.) that reside in folders on my harddisk.
Earlier I have tried to maintain a folder structure where material rests in specific folders based on content.
Lately I have thought about changing this, and to put all the files in a single folder, and organize them with tags instead of putting them in folders. This would allow me to assign more than one tag to a file, and a book like about RubyCocoa could then be tagged with “ruby”, “osx”, “cocoa”.
The best application I have found to organize tagged files is Leap. Instead of folders, I now have predefined searches that allow me quickly drill down to the files that I require. Leap has many more functions also, and allows drill-downs on file dates, types, size etc.