Probably it would be best to start our analysis by breaking down these stories into semiotic relationships as follows:
Signifier. One would think that Kafka himself, as the author, would be the signifier, but the term, as I understand it, is used in semiotics to designate the words or images that make up the narrative, or the manner in which the "sign" (the object of the story) is presented. In both "The Judgment" and "In the Penal Colony," Kafka gives us a low-key, matter-of-fact texturing of words that one would think might convey a harmless story without the dangerous and horrific results occurring here, especially in the latter story. In "The Judgment," the protagonist Georg's father suddenly freaks out and the relationship between father and son is laid bare in its dysfunctional nature. Similarly in "In the Penal Colony" the operation of the torture-and-death machine is methodically described as if it were an innocuous device for printing books, putting food in cans, or some other normal industrial process. That an actual person is being slowly tortured to death is the actual result. The act of signification is thus rendered as a form of irony.
Signified. The reality of what happens—violent familial conflict in the one case; sadistic enforcement of conformity by a governmental process in the other—is the actual object of the signifying, the "sign." But the signified is the ultimate theme or message of the story. What is it that Kafka is saying about human nature and the way familial relationships are conducted, or more broadly (and grimly) how those in power in despotic governments conduct themselves to their citizens? These questions, and the themes or messages implied by them, are arguably the objects of Kafka's signification.