By size and not at all. I have one shelf in the kitchen, and a few in the living room - those in the living room I need to sort by size, as some of the shelves aren't very high. Other than that, I don't sort them, as I use them too much to be bothered with putting them back in the correct order (and I never need to look for very long to find them, I guess that helps - I would probably spend more time sorting them than I do now looking for them). Also, sorting them by size means that I can't devise a proper sorting system anyway. I think I might try sorting them by topic otherwise.
I usually have six or seven that are out and accessible, and those are the ones I am generally using. The others are on a book case in a hodgepodge of organization that approximates topics (e.g. dessert cookbooks together).
I recently gathered cookbooks scattered through the house and discovered that I'm basically out of space for cookbooks. No more new ones for a while. :-(
I have some lovely book cases that house my cookbooks. Every once in a while I attempt to organize them. The top shelves are not as tall as the rest so they house the shorter and lesser used books. The other shelves are organized sort of by vague topics that only I would even begin to understand - baking, general cooking, cookbooks by bloggers or tv chefs, vegetarian, ethnic cookbooks. This system works fairly well and has greatly cut down on the time it takes me to find a cookbook that I need or am looking for.
All on shelves in the kitchen (apart from the ever-changing pile on the table of books I intend to use in the next couple of weeks) and basically alphabetical by author - not being able to sort them the same way on Cookbooker is about the only thing I don't like about this site. I do have two small separate sections - one for books about food that are not primarily cookery books (histories, essays &c) and one for "period" cookery books - both of which live on the highest and least accessible shelf.
Like Kaye16 I'm really running out of space, and I've had to grit my teeth and part with a few recently.
I have a bookcase just outside the kitchen with books I use regularly, and another big bookcase in the family room which is for general reference books but which nowadays principally houses culinary reference and history, as well as recipe books that I don't really use.
The two collections are arranged alphabetically by author because hubby was originally a librarian - only yesterday I was ticked off for putting my latest acquisition next to a very similar book. However he does let me keep my little Reaktion global histories all together, in alphabetical order of course.
And then there are the books that are just lying around the place because I haven't put them back and they're mixed up with the general books in progress. And I have a few on the iPad...
I have bookshelves in every room. I have one for male authors (in author's name alpha order) and one for female. These are general topic books. Then I have vegetarian bookshelves, author alpha order. One just for baking, author alpha order. Some cookbooks share with other subjects, each gets a shelf or two: cookies gets own shelf, cakes, etc. Restaurants/B&B's, etc get their own shelves. Community books are shelved by location, in order west coast to east coast. Entertainment gets its own area, healthy gets its own, ethnics get theirs, etc.
On computer, I use Calibre (or ebooks) and Readerware database for keeping track of hardcopy books..IF I have time to. And of course, Mastercook for all my 'done up' recipes, books, magazines.
I keep all ATK, BHG, Betty Crocker, etc. together on one bookshelf. Books about vegetables get their own shelf. Fruits stay with fruits.
(Yes, I've tried getting rid of books. I haul them to libraries, thrift shops, I've even put hundreds of them out front with FREE signs. But my addiction hasn't lessened and I still buy them whenever I hit the Goodwill or Amazon. It's an illness. I love it.)