By ISBN

Numerical order by the books' ISBN numbers. Very straightforward. Only complicated when you own older books, printed before the ISBN system. Order them by print year, perhaps?

By girth

One system that has been suggested to me: organizing the books by the number of pages.

I don't think I'll try this myself, as 1) it doesn't necessarily make it easy to find books, and 2) I'm afraid it would be symmetrical in the same sort of way as organizing by colour. Of course, there would be some asymmetry - books with the same amount of numbered pages can have very different girth, if they are in hardback or have very thin pages etc. But still.

Chronological orders

There are several different kinds of systems based on chronological order. Some are: By the author's birthday/age; By the year the book was written/published; By the order in which you bought/received the books; By the time in which the book is set.

1: By the author's birthday/age.
Complications:
* Books with two or more authors. But that should adhere to the general system: if you place your oldest authors first on your shelf, books with many authors should be ordered by the eldest - and vice versa.
* Authors with uncertain birthdays. And/or uncertain existence - like Homer.
* What do you mean: how old they were when they wrote the book, or how long ago they were born?!
Suborder: authors' books in order they were written.
Complication:
In the order they were written, or in the order they were published? These aren't always the same. Sub-complication if you choose the former: an author's old books are often extensively revised if they are published later in the author's career - is it the same book?

2. By the year the book was written/published.
Complication:
The same as above: what to do about revisions, and books where there is a long time between writing and publication? I would vote for [publishing date for the version at hand]. Revising a book is a lot of work.
Footnote: by version I mean version of text. If the paperback has the same text as the hardback, I'd go by the hardback's publication date.


3. By the order in which you bought or were given the books.
Complication:
I don't remember!! Do you?! If this were to work, I would've had to begun the system when I owned five books, and continued at it from then on. I know which ones I've owned for a long time, and which ones are new, but... srsly?

4. By the time in which the book is set.
Quite a challenge when you think of it. Could be interesting. What to do about alternate history/alternate reality, and time travel, and weaving together threads in several times, and books with huge time spans?

Would perhaps require separating books set in our world from books set in other worlds. Or would it? Here's one version that has been suggested: If a fantasy book is set in the year 3089 in its own world, it comes after e.g. 2001. Books where no year is mentioned are ordered by the season in chapter one. (But: what comes first, the winter or the egg? The spring or the chicken?)

But it might work, if I were to think it all through... Hmm...