Based on the journal, it sounded like Itakura was programming "The Thing" on his own before he was contacted by the Org, and then stopped because of his eye-sight. The Org later contacted him because they wanted him to restart work on the program. Itakura’s program is something an ordinary person would program; specifically someone who programmed games. It probably was a personal project of Itakura's as he was able to stop developing it on a whim; something he wouldn't be able to do so easily if he was paid to make it. If it is a personal project, it doesn't have to be specifically related to games. It could be something related to game development like artificial intelligence, networking, modeling, rendering, etc, or it could be something completely different. That the BO could find out about it in the first place probably indicates that Itakura didn't keep it secret. That means it probably not a virus or something highly illegal Itakura would not want to speak of, although modified it may have those applications.
Although I am not really confident with this, I believe that the computer research program is a project that is working towards the same goal as, but independent of, the APTX 4869 project. I have three main suspicions about what the Org is trying to do with the computer programming agenda.
One is to enhance the abilities of the mind through computer interfaces, basically to augment the brain with data stored on a computer. The problem here though is that this is a worthwhile goal, not something someone would not want to complete for the sake of humanity.
The second is to create a vast information and monitoring network. I got this idea from the Sherlock Holmes canon. "He [Moriarty] sits motionless, like a spider in the centre of its web, but that web has a thousand radiations, and he knows well every quiver of each of them". It would certainly help with crime, and would also fit the bill for being bad for humanity, but why would Itakura, a game programmer, be working on something like this to begin with, even if it was a personal project? Keep in mind Itakura's project likely wasn't secret.
The third theory is based on a recent suspicion that the Org's real goal is to be able to preserve one's mind eternally while maintaining mobility. One way to accomplish the goal would be to retard aging indefinitely - basically immortality which is what the biochem agenda is after IMO. Another way would to be able to create a perfect replica of the thought processes of a human on a computer, basically digitizing people. It is an AI based project, which fits for a game programmer, would require the smartest programmers known, and taken to a logical extreme becomes bad for humanity. However I also think it is also kind of "out there" for a theory.
So in conclusion, I don't know.