Like notebookpen, I first sort them by type. Then by authorname, and series. Books by the same author not in a series are mostly randomly put together. You could sort it by publishing date. Sometimes (like with tie-in novels) I sort them by series rather than author.
I would suggest looking at your collection and trying to find the biggest dividing lines. My system works for me because I have many different genres, and the biggest of them are easily divided into series.