In my room at home, I have three book cases plus two wall shelves. One book case is for theology and church history, one case is for fiction, and the last case continues the fiction, plus has the non-fiction that wouldn't (physically) fit on the shelves. The shelves are organized by history, science, and apologetics.
Within each category, I've organized the books by author. Fiction is organized by genre and then alphabetized -- except the Star Wars novels, which are in chronological order with the graphic novels at the end.
Here at school, I've got three shelves: class books, reference and miscellanea, and library books. They're not really organized beyond that because I couldn't really decide on a good system, though I've got my language books on one end and dictionaries (including foreign language) on the other end of the shelf, which makes it sort-of, kind-of, look as though I've arranged things by height.
EARTH smog | bricks AIR -- mud -- FIRE soda water | tequila WATER