Prior to the Great Book Move, the only books I had shelved in the open were my books on books and the (several) bookcases full of things recently acquired. The rest were living in the spare bedroom (now my bedroom), in basically no order whatever. Once the shelves were up and I could get everything out of storage, I had the wonderful (but troubling) dilemma of how to organize everything.
After much deliberation, I decided to start by shelving everything in order according to the Library of Congress classification scheme (since all my books are in LT, they already had LC numbers, or else I wouldn't even have considered this). I printed out an Excel list, started shelving, and quickly realized how quirky LC can be. On the whole I think it works, but boy is it counter-intuitive at times. More than once I had to check to make sure I was reading things right, thinking it impossible that books so seemingly different would be classed together (or that things that I thought should be adjacent would be in totally different areas).
I don't know that I'll leave my shelves in LC, but for now it does the job, and seems less subjective than anything I could come up with myself (which is not to say that it isn't subjective, since it clearly is ... catalogers are people too, after all).
It's always interesting (well, to me at least) to hear how other people organize their own books, so if you've got a scheme (or not) that works well for you (or doesn't), feel free to outline it in the comments. Anybody got the perfect system?
[Update: Just after I finished this, a post from Mrs. Bookworld crossed the transom - she's filling her nice new book-room, and offers her own musings on book organization (rather more coherent than mine, I think).]