Do we ever see or hear of this intelligent program again? Do any episodes, expanded universe novels, or even fan fiction stories tell of the fate of O'Brien's unwanted pet 'dog'?
Although it's never again mentioned in the TV series or films, the electronic virus known as the Pup does make a briefly appearance in the Trek Novel "Star Trek: Deep Space Nine: Valhalla" when O'Brien releases it in order to distract an electronic entity known as Enak who's taken over control of the station...
Instructions were being countermanded. Signals were being blocked. New software subroutines were interfering with Enak's orders.
Enak was losing control. The Pup was out of its doghouse and in Enak's virtual lap, and it had noticed that Enak was running the station. It wanted attention, wanted to play, so it was doing the cybernetic equivalent of jumping up and licking Enak's face.
Distracted, countered by one of its own distant relatives, Enak was unable to dominate the computer systems; it was kept busy just dealing with the Pup's friendly overtures.
At the end of the book, O'Brien returns it (apparently willingly) to its virtual 'doghouse'.