When I tell people that I'm in the process of writing The Torah Encyclopedia of the Animal Kingdom, they inevitably ask, "Which letter are you up to?"
It's a strange question. Or rather, it's a reasonable question that is based on a strange supposition.
Why would an encyclopedia be written in alphabetical order? The only benefit of such an arrangement is to assist in finding the relevant entry. But we have tables of contents and indexes that can do that.
Since the arrangement is not necessary to assist in locating information, it can be dedicated to other purposes - such as expressing concepts.
In this week's parashah, we have a list of non-kosher birds. It's not in alphabetical order. The nature of the order is not easy to determine, but it seems to be based around a decreasing order of prominence. That prominence itself seems to be based on a variety of factors, including size, prevalence, and degree of abnormality.
For my encyclopedia, the volumes are divided according to the system of classification used in the Torah - chayos, behemos, flying creatures, etc. And in the first volume, chayos, the animals are divided and ordered following conceptual patterns used in the Torah itself - predators, kosher animals, etc. Within each section, the order also follows patterns that appear in the Torah, as much as possible. The primary predators are listed in the same order as in Scripture and Mishnah; the minor predators are ordered according to size and prominence. The kosher wild animals are listed in the order in which they appear in parashas Re'ay, which itself is apparently based on their prevalence. And so on and so forth. You can download the table of contents here and see for yourself.
(Incidentally, I've almost completely finished the first volume - I just have to finish the entry on lions. And, of course, raise considerable funding!)