I'm another who only uses Calibre to convert and read the ebooks. I store them in folders on my computer. I've seen too many devastating problems with other programs to store mine there. As others have said, I sort into author's names (each in their own folder, first name in front, then by series if there is one. If an author has a second pen name, then I usually nest that inside the folder of the one I know better, unless they are so totally different that they're in their own.