Umberto Eco makes fun of working with index cards in Foucault’s Pendulum. Casaubon, the narrator in the novel, who is writing a dissertation on the medieval order of the Knights Templar, gets involved in a scheme based on the idea that the Templars have something to do with everything. He becomes “a kind of private eye of learning” and sets up a “cultural investigation agency.” When someone asks him to investigate, he goes to the library, flips through some catalogs, gives the “man in the reference office a cigarette, and picks up a clue” (224).
As he invents this job of cultural detective for himself, he muses: “I knew a lot of things, unconnected things, but I would be able to connect them after a few hours at a library. I once thought it was necessary to have a theory, and that my problem was that I didn't. But nowadays all you needed was information, especially if it was out of date” (223).
And, he tells us: “I was accumulating experience and information, and I never threw anything away. I kept files on everything. I didn't think to use a computer (they were coming on the market just then ... Instead, I had cross-referenced index cards. Nebulae, Laplace; Laplace, Kant; Kant, Königsberg, the seven bridges problem of Königsberg, theorems of topology ... It was a little like that game where you have to go from sausage to Plato in five steps, by association of ideas. Let's see: sausage, pig bristle, paintbrush, Mannerism, Idea, Plato. Easy. Even the sloppiest manuscript would bring twenty new cards for my hoard. I had a strict rule, which I think secret services follow, too: No piece of information is superior to any other. Power lies in having them all on file and then finding the connections. There are always connections; you have only to want to find them." 
In some sense, the whole book is about making connections by associations that might appear reckless to the contemporary reader, but which would have made a great deal of sense to many Renaissance thinkers. The book is strewn with references to such thinkers and the way they used analogies. One gets the distinct impression that the book owes much of its wild learnedness to the use of “cross-referenced index cards,” the idea that “no piece of information is superior to any other,” and the idea that “there are always connections.” So, the passage certainly may be read as poking fun at the novel itself.
The passage may also be read as a parody of Umberto Eco, the semiotician himself, who once thought he needed a theory, and who wrote in 1977 a book called Come si fa una tesi di laurea (How to make a doctoral thesis), in which he described in great detail for students how one should use index cards in writing a scholarly essay. 
I don’t know whether Eco knew Luhmann’s index card method. But whether or not he knew it, the principles he outlines have a great deal of affinity with those of Luhmann, i.e. (i) every card has not significance in isolation, but gets it from its connections with all the others, (ii) there is no privileged card (or place) in the system, that, (iii) the power of this system lies in having information on file that is retrievable, and that (iv) the finding of the connections might involve serendipity.
But perhaps it is just me who under the influence of the book begins to believe that everything bears relationships of analogy, contiguity and similarity to everything else, which is the basic principle of all conspiratorial thought.
I recoil in horror!
1. I use the English translation by William Weaver (New York: Harcourt Brace Jovanovich, Publishers). I am not sure how reliable it is, as I don’t have the Italian. But the German text sounds rather different, speaking of the card index as “a kind of artificial (independent) memory” and characterizing it as “cross-referenced and networked.”
See also p. 618: Where the rules of “the game” that’s played in the novel are explained: “In a crossword puzzle the words intersecting, have to have letters in common. In our game we crossed not only words but concepts, events, so the rules were different. Basically there were three rules.
Rule One: Concepts are connected by analogy. There is no way to decide at once whether an analogy is good or bad, because to some degree everything is connected to everything else. For example, potato crosses with apple, because both are vegetable and round in shape. From apple to snake, by Biblical association. From snake to doughnut, by formal likeness. From doughnut to life preserver, and from live preserver to bathing suit ... [etc. etc.] hole to ground, ground to potato.
Rule Two says that if tout se tient in the end, the connecting works. From potato to potato, tout se tient. So it’s right.
Rule Three: The connection must not be original. They must have been made before, and the more often the better ..."
And here are many other passages about connections and association. Some of them are more historical and to be taken more seriously.
2. I have only consulted the German translation: Wie man eine wissenschaftliche Abschlussarbeit schreibt: Doktor-, Diplom- und Magisterarbeit in den Geistes- und Sozialwissenschaften. 9. unveränd. Aufl. der dt. Ausg. Heidelberg: UTB Uni-Taschenbücher Verlag.