To keep notes (or any kind of information) in the order of the alphabet, without any attempt to order it systematically has seemed unnatural to many thinkers: The world is a cosmos, it has a natural order or ordo that comes from God or from reason. The idea of an ordo rationis that expresses the way things are in themselves is at least as old as Aristotle's philosophy. According to such a theory, "to order" means therefore neither to organize and systematize knowledge according to our preconceptions or purposes. Nor does it mean to "manage" it. Rather, it is the interiorization of the order that is cosmic and symbolic at the same time. "It was one of the fundamental character traits of the early Christian and medieval mentalities that the signifying, symbolizing, and allegorizing function was anything but arbitrary or subjective; symbols were believed to represent objectively and to express faithfully various aspects of a universe that was perceived as widely and deeply meaningful." (See Ivan Illich, In the Vineyard of the Text. A Commentary on Hugh's Didascalicon. Chicago: University of Chicago Press, 1993).
One of the last writers to attack alphabetical order was Mortimer Adler, who wrote much of his A Guidebook to Learning: For the Lifelong Pursuit of Wisdom to criticizing alphabetical order and arguing that "resorting solely to the alphabet" amounts to "intellectual dereliction" and "an aversion of intellectual reponsibility." But there are many others who have objected to alphabetization on similar grounds.
It is easy to dismiss such a view as a relic of the past. But there is, it appears to me, no need to do so. Adler was missing the wrong target. Listing or presenting things in the order of the alphabet does not imply that there is no other order. Alphabetization does not even imply that we do not or could not know any other order, even though some suggest as much. All it means is that for some purposes alphabetization is more convenient and useful. The same holds for ordering things or ideas according to some numerical scheme (such as the one proposed by Luhmann for his Zettelkasten). Pace, Luhmann, I would claim that such ordering schemes may with equal justification be thought of as helps in discovering the true order of the universe as they may be seen as tools that express our subjective or social needs. Per se, they are neutral as to the ontological structure of the world, unless we explicitly wish to make them relevant in this way.
The same holds, of course, for links and tags. The fact that hypertextual and wiki links are useful for keeping notes or for presenting information does not necessarily imply anything about the nature of the universe. The same things holds for tags. David Weinberger argues in Everything is Miscellaneous. The Power of the New Digital Disorder (New York: Times Books, 2007) that they provide a new order of order. This may well be true. It may well be that "for the first time we have an infrastructure that allows us to hop over and around established categorizations with ease," but this does not invalidate the idea that there is an order of the world that is independent of this infrastructure - however difficult this fundamental order may be to determine. What's wrong with Adler's view is that it involves a much too simple idea of what the order of the universe must be.