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For my printed paper music, I put the sheet music/song sheets alphabetically by song title. I used to keep them in a binder but now I have so many that I keep them in folders. Right now I have A-M in one, N-Z in another one, and I do keep any alternate tuning songs in another folder, arranged by which tuning the song is in. (DADGAD, Open G, Open D, Etc)
I also keep one or 2 binders with plastic page protectors, for taking selected loose music out with me to jam parties, guitar camps etc.
I also have a whole library of guitar song books, workbooks and stuff like that. I have them all on the shelf arranged by topic (classical, theory, instructional, fingerstyle, christmas, etc.)
It took me 2 full days to organize all of my music last summer but it was well worth it. Now I can find stuff within 2 minutes and know if I have the music or not. 🙂