Over the years I have displayed the books in just about every sequence I could think of. US trades, foreign trades and S/L's together by title, proofs separate from trades, etc. The only thing I think I haven't done is alphabetical by title (that would be too weird). My present display order is the one that is most pleasing to me and makes more sense to me but each collector gets to decide that for himself.
I have a system in place for magazines and college stuff in the back room. It's not the most visually pleasing part of my collection but it is functional.