Method #1 -- The Notebook System
One way to store the music is by using poly page protector sleeves to keep each piece of music separately. The sleeves will accommodate up to the standard 8.5x11 sheets of paper, but can hold octavos as well. It's a good idea to have the pieces organized alphabetically within the notebook to aid in quick look up by title.
Another way to use the page protectors is to put two sheets per sleeve, back-to-back (or one sheet printed on both sides), so that all the music is readable as you flip through the notebook. This is more practical for piano accompanists and other live performance applications. This way, you don't have to remove the sheet music from the sleeve in order to read it. When using the music for performance, it is best to have it arranged in concert order rather than alphabetically.
The third way to organize music in a notebook is to hole punch the actual sheets and clip them directly into the notebook. This saves the extra step of putting the sheets into the page protectors and also saves on weight if you have to hold the notebook for an extended period. It is helpful to have some sort of divider between songs with this method, and a simple brightly colored sheet of paper (also 3-hole punched) between pieces is often enough to give a division.
Method #2 -- The File System
Marking or labeling the folders makes finding them much easier. My favorite way to label folders is the P-Touch System that I fell in love with when I was filing documents every day in an office job. The drawback to these labels is that they are pretty expensive if you use it a lot. However, the clean typed text is much nicer than my chicken-scratch handwriting and makes the labels easier to read and the files look much more professional.
I also use the filing system for storing music for small groups that I sing with, such as the men's quartet at church that I referred to in my article yesterday. I have each of our current songs in its own manila folder, with each individual copy of the song paper clipped. All of the current songs we are working on are in one hanging folder, and songs that are part of our past repertoire in another. This way I can grab the current song folders on my way to rehearsal, distribute the copies of each song quickly, and keep the music organized so that our practice time is not spent trying to sort out the music that we need.
So there you have it! I hope that you will be able to use these simple ideas to make your sheet music organization easier and more efficient. If you have other ideas that may be helpful, please share a comment.