Lifehacker ran an article (here) on organising your bookshelves that I thought might help me out. However, as I have literally thousands of books I think I need to move house before I can even *put* them all on bookshelves, let along organise them. I digress. One of the comments led me to the Sorted Books project from Nina Katchadourian. In her words:
"The process is the same in every case: culling through a collection of books, pulling particular titles, and eventually grouping the books into clusters so that the titles can be read in sequence, from top to bottom."
Love it - some examples are very witty and I just wish I'd thought of it!