Chad's got an excellent post called "You Are What You Appear to Have Read," although I have to say that I violate most of the prime directives of book-shelving no matter what system you think best. I don't have any photographs of the present arrangement, but being that I'm living in an apartment space is at a premium. There are three main bookshelves that just barely hold all the books my wife and I had acquired up until about last week (we've even doubled up with the paperbacks to fit more in), but a recent trip to the Cranbury Bookworm means that there are now about 30 new (old?) books lying on the floor with nowhere to go.
Eventually I hope to have a study, filled with books, fossils, and bones, but for now I've got to work with what I have. Rather than alphabetize my books, though, I have a general system that wouldn't make sense to anyone else but me. The bookshelf next to my bed is primarily by paleontology, anthropology, history of science, and old 19th/early 20th century science books that I like to have close at hand. Generally my favorite non-fiction books live on these shelves, although a few sometimes get shuffled around. On another shelf across the room are books about ecology, zoology, and African wildlife, and a few shelves up is most of my small collection of creationist literature (letting them mingle with the science books would be an abomination).
The top of the entertainment center holds a lot of old textbook and coffee-table books about the ocean/sharks, and some books that I didn't particularly like (but might come in handy) are shoved in random places. Given that I plan on living in my present location for another year, though, I don't know where any new acquisitions are going to live. Eventually they'll all have a good home, but for now utility is the name of the game.
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All of the fiction books my husband and I own are in alphabetical order by author, sort of, (except for books that I haven't read yet which are in their own section) but the non-fiction is organized by subject matter. This may not be ideal, but it's the system that works best for us. We've sort of outgrown the shelves, though, and the fiction paperbacks are stacked vertically on some shelves--in two layers--and the larger non-fiction books are getting piled into corners. We don't have much space for more shelves, though....
Ditto about the study. But without the bones. I've always envisioned a molecular model of DNA and random ancient astronomical devices.
I love the study filled with books and bones concept. I've been hinting to my girlfriend that I really need one of bone clones Smilodon replicas for my office space - unsuccessfully thus far!