The organization of multiple files, whether digitized or on paper, has always been a challenge. There seem to be two main camps; on the one hand there are those who want to duplicate their paper file organization on the computer, using the desktop metaphor of files and file folders. Otherwise, there are those who recognize that computers do not need a file metaphor and they use the computer to "organize" the files. Admittedly, using the computer to do the organization is pretty technical. But you might find the optimal way to organize your files somewhere between the two extremes.
I assume that because the paper file/computer file metaphor is so pervasive in the graphic user interface of all of today's consumer computers, that this is the most likely way that genealogists will start to organize on the computer. In this method, you create a new file folder at some location on the computer, say for a surname, and then start putting sub-files into the surname folder. You then create sub-folders for each of the succeeding generation's surnames. In essence you are recreating the structure of a pedigree chart using the hierarchical file system of the computer's operating system. To find a document, you start down through the file structure until you identify the related surname and then hopefully, the information you are look for is located in that folder. This system is essentially the same whether you organize your folders according to surname, location, or some other criteria. Either way, you end up with nested folders related to one another due to their location in some other folder.
The essence of this type of organization is spatial. I have one family in the blue folders and another in the yellow folders. Each person's virtual folder is a duplicate of what would go into a paper folder in a physical file drawer. This type of filing system is very efficient up to a certain size level. Think of a doctor's office with their filing system of multicolored tabs. The number of file folders can become overwhelmingly large. No matter how reasonable and rational your system of duplicating paper files, you will still have an unworkable system if your database is very large. For example, what if your relatives all lived in the same place and knew each other (not that uncommon)? Do you have to make copies of every document for each folder in each line, assuming the families are all mentioned in the document? (Such as a Census Page).
As you can probably tell, I am not a fan of paper filing systems. I have spent too many days and months of my life looking for lost physical files. This whole system presupposes that you can keep track of what kind of file each kind of document should be filed in. But what if you have a general background document that has no specific relationship to any one file? Where does it go? Simple, you say, just create a general document file. At some point, file folders become the issue not the solution.
Now, what do you do if you let the computer do all the filing and sorting? You identify each document individually with a date, and a file number (arbitrary) and key words. You then attach the documents to each individual they pertain to by using the media function available in all current genealogical databases. You do not put the documents into separate file folders. You leave them all in one huge pile on the computer and then use the computer to find the documents based on the individual and unique meta-data (extra information) about each file document. I use a program called Adobe Bridge, this lets me add key words to any file. I can also add Spotlight comments to my files using the Apple OS X operating system.
Key words might include the date, time and place of the document, the names of all of the people mentioned and general descriptive words, such as probate, will, witness, etc. Then use the computer to search for the document using those key words. There is hopefully, only one copy of each document stored on your computer. You don't worry about where the document is stored, it is always in the right place, exactly where you left it and can be opened at any time.
If you are going to use the computer to organize your files, you need some way to store meta-data with your files. Both Apple and Microsoft allow you to add key words to file data, but a program like Adobe Bridge is more efficient.