I use the Dewey Decimal System for my non-fiction books and alpha-by-author's last name (with chronological for series) for fiction. A simple spreadsheet with DDS#, Title, Author, Shelf/Room, Loaned To, and Loaned On does the organization for me. I could print out barcodes and get a scanner if I wanted to get fancy.
For my ebooks, I back them up into Non-Fiction or Fiction folders with the non-fiction subfolders being subject (science, history, etc) and the subfolders for fiction being author's name.